Revision ef04f11c
Added by Andreas Müller over 11 years ago
app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraSpecimenImport.java | ||
---|---|---|
26 | 26 |
|
27 | 27 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
28 | 28 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType; |
29 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException; |
|
29 | 30 |
import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraSpecimenImportValidator; |
30 | 31 |
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase; |
31 | 32 |
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator; |
... | ... | |
41 | 42 |
import eu.etaxonomy.cdm.model.common.Marker; |
42 | 43 |
import eu.etaxonomy.cdm.model.common.MarkerType; |
43 | 44 |
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary; |
45 |
import eu.etaxonomy.cdm.model.common.TermVocabulary; |
|
44 | 46 |
import eu.etaxonomy.cdm.model.common.TimePeriod; |
45 | 47 |
import eu.etaxonomy.cdm.model.description.CategoricalData; |
46 | 48 |
import eu.etaxonomy.cdm.model.description.DescriptionBase; |
47 | 49 |
import eu.etaxonomy.cdm.model.description.Feature; |
48 | 50 |
import eu.etaxonomy.cdm.model.description.IndividualsAssociation; |
51 |
import eu.etaxonomy.cdm.model.description.MeasurementUnit; |
|
52 |
import eu.etaxonomy.cdm.model.description.Modifier; |
|
53 |
import eu.etaxonomy.cdm.model.description.QuantitativeData; |
|
49 | 54 |
import eu.etaxonomy.cdm.model.description.SpecimenDescription; |
50 | 55 |
import eu.etaxonomy.cdm.model.description.State; |
56 |
import eu.etaxonomy.cdm.model.description.StatisticalMeasure; |
|
57 |
import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue; |
|
51 | 58 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
52 | 59 |
import eu.etaxonomy.cdm.model.description.TextData; |
53 | 60 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
... | ... | |
57 | 64 |
import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry; |
58 | 65 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
59 | 66 |
import eu.etaxonomy.cdm.model.name.Rank; |
67 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
|
60 | 68 |
import eu.etaxonomy.cdm.model.occurrence.FieldObservation; |
61 | 69 |
import eu.etaxonomy.cdm.model.reference.Reference; |
62 | 70 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
... | ... | |
72 | 80 |
public class AlgaTerraSpecimenImport extends BerlinModelImportBase { |
73 | 81 |
private static final Logger logger = Logger.getLogger(AlgaTerraSpecimenImport.class); |
74 | 82 |
|
75 |
public static final String FIELD_OBSERVATION_NAMESPACE = "FieldObservation";
|
|
83 |
public static final String ECO_FACT_NAMESPACE = "EcoFact";
|
|
76 | 84 |
public static final String TERMS_NAMESPACE = "ALGA_TERRA_TERMS"; |
77 | 85 |
|
78 |
//move to transformrer |
|
86 |
//TODO move to transformrer
|
|
79 | 87 |
final static UUID uuidMarkerAlkalinity = UUID.fromString("e52d0ea2-0c1f-4d95-ae6d-e21ab317c594"); |
80 | 88 |
final static UUID uuidRefSystemGps = UUID.fromString("c23e4928-c137-4e4a-b6ab-b430da3d0b94"); |
81 | 89 |
final static UUID uuidFeatureSpecimenCommunity = UUID.fromString("3ff5b1ab-3999-4b5a-b8f7-01fd2f6c12c7"); |
82 | 90 |
final static UUID uuidFeatureAdditionalData = UUID.fromString("0ac82ab8-2c2b-4953-98eb-a9f718eb9c57"); |
91 |
final static UUID uuidFeatureHabitatExplanation = UUID.fromString("6fe32295-61a3-44fc-9fcf-a85790ea888f"); |
|
83 | 92 |
|
84 | 93 |
final static UUID uuidVocAlgaTerraClimate = UUID.fromString("b0a677c6-8bb6-43f4-b1b8-fc377a10feb5"); |
85 | 94 |
final static UUID uuidVocAlgaTerraHabitat = UUID.fromString("06f30114-e19c-4e7d-a8e5-5488c41fcbc5"); |
... | ... | |
89 | 98 |
final static UUID uuidFeatureAlgaTerraHabitat = UUID.fromString("7def3fc2-cdc5-4739-8e13-62edbd053415"); |
90 | 99 |
final static UUID uuidFeatureAlgaTerraLifeForm = UUID.fromString("9b657901-1b0d-4a2a-8d21-dd8c1413e2e6"); |
91 | 100 |
|
101 |
final static UUID uuidVocParameter = UUID.fromString("45888b40-5bbb-4293-aa1e-02479796cd7c"); |
|
102 |
final static UUID uuidStatMeasureSingleValue = UUID.fromString("eb4c3d98-4d4b-4c37-8eb4-17315ce79920"); |
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103 |
final static UUID uuidMeasurementValueModifier = UUID.fromString("0218a7a3-f6c0-4d06-a4f8-6b50b73aef5e"); |
|
92 | 104 |
|
105 |
final static UUID uuidModifierLowerThan = UUID.fromString("2b500085-6bef-4003-b6ea-e0ad0237d79d"); |
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106 |
final static UUID uuidModifierGreaterThan = UUID.fromString("828df49d-c745-48f7-b083-0ada43356c34"); |
|
93 | 107 |
|
94 | 108 |
private static int modCount = 5000; |
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private static final String pluralString = "specimen and observation"; |
... | ... | |
154 | 168 |
Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>(); |
155 | 169 |
|
156 | 170 |
Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE); |
157 |
Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>) partitioner.getObjectMap(FIELD_OBSERVATION_NAMESPACE);
|
|
171 |
Map<String, DerivedUnit> ecoFactMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(ECO_FACT_NAMESPACE);
|
|
158 | 172 |
|
159 | 173 |
ResultSet rs = partitioner.getResultSet(); |
160 | 174 |
|
... | ... | |
178 | 192 |
Reference<?> sourceRef = state.getTransactionalSourceReference(); |
179 | 193 |
|
180 | 194 |
//facade |
181 |
FieldObservation fieldObservation = getFieldObservation(ecoFactId, fieldObservationMap); |
|
182 | 195 |
DerivedUnitType type = makeDerivedUnitType(recordBasis); |
183 |
DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(type, fieldObservation);
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|
184 |
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|
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DerivedUnitFacade facade = getDerivedUnit(state, ecoFactId, ecoFactMap, type);
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|
|
185 | 198 |
//field observation |
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handleSingleSpecimen(rs, facade, state); |
187 | 200 |
|
201 |
state.setCurrentFieldObservationNotNew(false); |
|
202 |
|
|
188 | 203 |
//description element |
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TaxonDescription taxonDescription = getTaxonDescription(state, newTaxonId, taxonMap, factId, sourceRef); |
190 | 205 |
IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance(); |
... | ... | |
295 | 310 |
|
296 | 311 |
|
297 | 312 |
private void handleSingleSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state) throws SQLException { |
298 |
//CollectionFk, Collector, AltitudeMethod, |
|
299 |
//ISOCountrySub, CreatedWhen/Who/Updated/who |
|
300 |
|
|
301 |
//P1-10Value/Unit/Parameter/Method |
|
302 |
|
|
313 |
//FIXME missing fields #3084, #3085, #3080 |
|
303 | 314 |
try { |
304 | 315 |
Object alkalinityFlag = rs.getBoolean("AlkalinityFlag"); |
305 | 316 |
|
... | ... | |
329 | 340 |
|
330 | 341 |
|
331 | 342 |
|
332 |
FieldObservation fieldObservation = facade.innerFieldObservation();
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|
343 |
FieldObservation fieldObservation = facade.getFieldObservation(true);
|
|
333 | 344 |
|
334 | 345 |
//alkalinity marker |
335 | 346 |
if (alkalinityFlag != null){ |
... | ... | |
376 | 387 |
|
377 | 388 |
//habitat, ecology, community, etc. |
378 | 389 |
DescriptionBase<?> fieldDescription = getFieldObservationDescription(facade); |
390 |
|
|
379 | 391 |
addCategoricalValue(state, fieldDescription, climateUuid, uuidFeatureAlgaTerraClimate); |
380 | 392 |
addCategoricalValue(state, fieldDescription, habitatUuid, Feature.HABITAT().getUuid()); |
381 | 393 |
addCategoricalValue(state, fieldDescription, lifeFormUuid, uuidFeatureAlgaTerraLifeForm); |
382 | 394 |
|
383 | 395 |
if (isNotBlank(habitat)){ |
384 |
//FIXME |
|
385 |
facade.setEcology(habitat); //or use an own feature ?? |
|
396 |
Feature habitatExplanation = getFeature(state, uuidFeatureHabitatExplanation, "Habitat Explanation", "HabitatExplanation", null, null); |
|
397 |
TextData textData = TextData.NewInstance(habitatExplanation); |
|
398 |
textData.putText(Language.DEFAULT(), habitat); |
|
399 |
getFieldObservationDescription(facade).addElement(textData); |
|
386 | 400 |
} |
387 | 401 |
if (isNotBlank(community)){ |
388 | 402 |
Feature communityFeature = getFeature(state, uuidFeatureSpecimenCommunity, "Community", "The community of a specimen (e.g. other algae in the same sample)", null, null); |
... | ... | |
407 | 421 |
makeAreas(state, rs, facade); |
408 | 422 |
|
409 | 423 |
//parameters |
410 |
//TODO
|
|
424 |
makeParameter(state, rs, getFieldObservationDescription(facade));
|
|
411 | 425 |
|
412 | 426 |
//collection |
413 | 427 |
String voucher = rs.getString("Voucher"); |
... | ... | |
422 | 436 |
//TODO id, created for fact + ecoFact |
423 | 437 |
// this.doIdCreatedUpdatedNotes(state, descriptionElement, rs, id, namespace); |
424 | 438 |
|
425 |
} catch (IllegalArgumentException e) {
|
|
426 |
throw e;
|
|
439 |
} catch (Exception e) { |
|
440 |
throw new RuntimeException(e);
|
|
427 | 441 |
} |
428 | 442 |
|
429 | 443 |
} |
430 | 444 |
|
431 | 445 |
|
446 |
private void makeParameter(AlgaTerraImportState state, ResultSet rs, DescriptionBase<?> descriptionBase) throws SQLException { |
|
447 |
for (int i = 1; i <= 10; i++){ |
|
448 |
String valueStr = rs.getString(String.format("P%dValue", i)); |
|
449 |
String unitStr = rs.getString(String.format("P%dUnit", i)); |
|
450 |
String parameter = rs.getString(String.format("P%dParameter", i)); |
|
451 |
String method = rs.getString(String.format("P%dMethod", i)); |
|
452 |
|
|
453 |
//method |
|
454 |
if (StringUtils.isNotBlank(method)){ |
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logger.warn("Methods not yet handled: " + method); |
|
456 |
} |
|
457 |
//parameter |
|
458 |
TermVocabulary<Feature> vocParameter = getVocabulary(uuidVocParameter, "Feature vocabulary for AlgaTerra measurement parameters", "Parameters", null, null, false, Feature.COMMON_NAME()); |
|
459 |
if (StringUtils.isNotBlank(parameter)){ |
|
460 |
UUID featureUuid = getParameterFeatureUuid(state, parameter); |
|
461 |
Feature feature = getFeature(state, featureUuid, parameter, parameter, null, vocParameter); |
|
462 |
QuantitativeData quantData = QuantitativeData.NewInstance(feature); |
|
463 |
|
|
464 |
//unit |
|
465 |
MeasurementUnit unit = getMeasurementUnit(state, unitStr); |
|
466 |
quantData.setUnit(unit); |
|
467 |
try { |
|
468 |
|
|
469 |
Set<Modifier> valueModifier = new HashSet<Modifier>(); |
|
470 |
valueStr = normalizeAndModifyValue(state, valueStr, valueModifier); |
|
471 |
//value |
|
472 |
Float valueFlt = Float.valueOf(valueStr); //TODO maybe change model to Double ?? |
|
473 |
|
|
474 |
StatisticalMeasure measureSingleValue = getStatisticalMeasure(state, uuidStatMeasureSingleValue, "Value", "Single measurement value", null, null); |
|
475 |
StatisticalMeasurementValue value = StatisticalMeasurementValue.NewInstance(measureSingleValue, valueFlt); |
|
476 |
quantData.addStatisticalValue(value); |
|
477 |
descriptionBase.addElement(quantData); |
|
478 |
|
|
479 |
} catch (NumberFormatException e) { |
|
480 |
logger.warn(String.format("Value '%s' can't be converted to double. Parameter %s not imported.", valueStr, parameter)); |
|
481 |
} |
|
482 |
}else if (isNotBlank(valueStr) || isNotBlank(unitStr) ){ |
|
483 |
logger.warn("There is value or unit without parameter: " + i); |
|
484 |
} |
|
485 |
|
|
486 |
|
|
487 |
} |
|
488 |
|
|
489 |
} |
|
490 |
|
|
491 |
private String normalizeAndModifyValue(AlgaTerraImportState state, String valueStr, Set<Modifier> valueModifier) { |
|
492 |
valueStr = valueStr.replace(",", "."); |
|
493 |
if (valueStr.startsWith("<")){ |
|
494 |
TermVocabulary<Modifier> measurementValueModifierVocabulary = getVocabulary(uuidMeasurementValueModifier, "Measurement value modifier", "Measurement value modifier", null, null, false, Modifier.NewInstance()); |
|
495 |
Modifier modifier = getModifier(state, uuidModifierLowerThan, "Lower", "Lower than the given measurement value", "<", measurementValueModifierVocabulary); |
|
496 |
valueModifier.add(modifier); |
|
497 |
valueStr = valueStr.replace("<", ""); |
|
498 |
} |
|
499 |
if (valueStr.startsWith(">")){ |
|
500 |
TermVocabulary<Modifier> measurementValueModifierVocabulary = getVocabulary(uuidMeasurementValueModifier, "Measurement value modifier", "Measurement value modifier", null, null, false, Modifier.NewInstance()); |
|
501 |
Modifier modifier = getModifier(state, uuidModifierGreaterThan, "Lower", "Lower than the given measurement value", "<", measurementValueModifierVocabulary); |
|
502 |
valueModifier.add(modifier); |
|
503 |
valueStr = valueStr.replace(">", ""); |
|
504 |
} |
|
505 |
return valueStr; |
|
506 |
} |
|
507 |
|
|
508 |
|
|
509 |
|
|
510 |
private UUID getParameterFeatureUuid(AlgaTerraImportState state, String key) { |
|
511 |
//TODO define some UUIDs in Transformer |
|
512 |
UUID uuid = state.getParameterFeatureUuid(key); |
|
513 |
if (uuid == null){ |
|
514 |
uuid = UUID.randomUUID(); |
|
515 |
state.putParameterFeatureUuid(key, uuid); |
|
516 |
} |
|
517 |
return uuid; |
|
518 |
} |
|
519 |
|
|
520 |
|
|
521 |
|
|
522 |
/** |
|
523 |
* TODO move to InputTransformerBase |
|
524 |
* @param state |
|
525 |
* @param unitStr |
|
526 |
* @return |
|
527 |
*/ |
|
528 |
private MeasurementUnit getMeasurementUnit(AlgaTerraImportState state, String unitStr) { |
|
529 |
MeasurementUnit result = null; |
|
530 |
if (StringUtils.isNotBlank(unitStr)){ |
|
531 |
UUID uuidMeasurementUnitMgL = UUID.fromString("7ac302c5-3cbd-4334-964a-bf5d11eb9ead"); |
|
532 |
UUID uuidMeasurementUnitMolMol = UUID.fromString("96b78d78-3e49-448f-8100-e7779b71dd53"); |
|
533 |
UUID uuidMeasurementUnitMicroMolSiL = UUID.fromString("2cb8bc85-a4af-42f1-b80b-34c36c9f75d4"); |
|
534 |
UUID uuidMeasurementUnitMicroMolL = UUID.fromString("a631f62e-377e-405c-bd1a-76885b13a72b"); |
|
535 |
UUID uuidMeasurementUnitDegreeC = UUID.fromString("55222aec-d5be-413e-8db7-d9a48c316c6c"); |
|
536 |
UUID uuidMeasurementUnitPercent = UUID.fromString("3ea3110e-f048-4bed-8bfe-33c60f63626f"); |
|
537 |
UUID uuidMeasurementUnitCm = UUID.fromString("3ea3110e-f048-4bed-8bfe-33c60f63626f"); |
|
538 |
UUID uuidMeasurementUnitMicroSiCm = UUID.fromString("3ea3110e-f048-4bed-8bfe-33c60f63626f"); |
|
539 |
|
|
540 |
|
|
541 |
if (unitStr.equalsIgnoreCase("mg/L")){ |
|
542 |
return getMeasurementUnit(state, uuidMeasurementUnitMgL, unitStr, unitStr, unitStr, null); |
|
543 |
}else if (unitStr.equalsIgnoreCase("mol/mol")){ |
|
544 |
return result = getMeasurementUnit(state, uuidMeasurementUnitMolMol, unitStr, unitStr, unitStr, null); |
|
545 |
}else if (unitStr.equalsIgnoreCase("\u00B5mol Si/L")){ //µmol Si/L |
|
546 |
return getMeasurementUnit(state, uuidMeasurementUnitMicroMolSiL, unitStr, unitStr, unitStr, null); |
|
547 |
}else if (unitStr.equalsIgnoreCase("\u00B5mol/L")){ //µmol/L |
|
548 |
return getMeasurementUnit(state, uuidMeasurementUnitMicroMolL, unitStr, unitStr, unitStr, null); |
|
549 |
}else if (unitStr.equalsIgnoreCase("\u00B0C")){ //°C |
|
550 |
return getMeasurementUnit(state, uuidMeasurementUnitDegreeC, unitStr, unitStr, unitStr, null); |
|
551 |
}else if (unitStr.equalsIgnoreCase("%")){ |
|
552 |
return getMeasurementUnit(state, uuidMeasurementUnitPercent, unitStr, unitStr, unitStr, null); |
|
553 |
}else if (unitStr.equalsIgnoreCase("cm")){ |
|
554 |
return getMeasurementUnit(state, uuidMeasurementUnitCm, unitStr, unitStr, unitStr, null); |
|
555 |
}else if (unitStr.equalsIgnoreCase("\u00B5S/cm")){ //µS/cm |
|
556 |
return getMeasurementUnit(state, uuidMeasurementUnitMicroSiCm, unitStr, unitStr, unitStr, null); |
|
557 |
}else{ |
|
558 |
logger.warn("MeasurementUnit was not recognized"); |
|
559 |
return null; |
|
560 |
} |
|
561 |
}else{ |
|
562 |
return null; |
|
563 |
} |
|
564 |
} |
|
565 |
|
|
566 |
|
|
567 |
|
|
432 | 568 |
private void addCategoricalValue(AlgaTerraImportState importState, DescriptionBase description, String uuidTerm, UUID featureUuid) { |
433 | 569 |
if (uuidTerm != null){ |
434 | 570 |
State state = this.getStateTerm(importState, UUID.fromString(uuidTerm)); |
... | ... | |
539 | 675 |
} |
540 | 676 |
} |
541 | 677 |
|
542 |
private FieldObservation getFieldObservation(int ecoFactId, Map<String, FieldObservation> fieldObservationMap) { |
|
678 |
/** |
|
679 |
* @param state |
|
680 |
* @param ecoFactId |
|
681 |
* @param derivedUnitMap |
|
682 |
* @param type |
|
683 |
* @return |
|
684 |
*/ |
|
685 |
private DerivedUnitFacade getDerivedUnit(AlgaTerraImportState state, int ecoFactId, Map<String, DerivedUnit> derivedUnitMap, DerivedUnitType type) { |
|
543 | 686 |
String key = String.valueOf(ecoFactId); |
544 |
FieldObservation fieldObservation = fieldObservationMap.get(key); |
|
545 |
if (fieldObservation == null){ |
|
546 |
fieldObservation = FieldObservation.NewInstance(); |
|
547 |
|
|
548 |
fieldObservationMap.put(key, fieldObservation); |
|
687 |
DerivedUnit derivedUnit = derivedUnitMap.get(key); |
|
688 |
DerivedUnitFacade facade; |
|
689 |
if (derivedUnit == null){ |
|
690 |
facade = DerivedUnitFacade.NewInstance(type); |
|
691 |
derivedUnitMap.put(key, derivedUnit); |
|
692 |
}else{ |
|
693 |
try { |
|
694 |
facade = DerivedUnitFacade.NewInstance(derivedUnit); |
|
695 |
} catch (DerivedUnitFacadeNotSupportedException e) { |
|
696 |
logger.error(e.getMessage()); |
|
697 |
facade = DerivedUnitFacade.NewInstance(type); |
|
698 |
} |
|
549 | 699 |
} |
550 | 700 |
|
551 |
return fieldObservation;
|
|
701 |
return facade;
|
|
552 | 702 |
} |
553 | 703 |
|
554 | 704 |
private Feature makeFeature(DerivedUnitType type) { |
... | ... | |
616 | 766 |
result.put(nameSpace, objectMap); |
617 | 767 |
|
618 | 768 |
//field observation map map |
619 |
nameSpace = AlgaTerraSpecimenImport.FIELD_OBSERVATION_NAMESPACE;
|
|
769 |
nameSpace = AlgaTerraSpecimenImport.ECO_FACT_NAMESPACE;
|
|
620 | 770 |
cdmClass = FieldObservation.class; |
621 | 771 |
idSet = taxonIdSet; |
622 | 772 |
Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
Also available in: Unified diff
latest updates for ALgaterra import