Revision bb38665e
Added by Andreas Müller over 10 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraSpecimenImportBase.java | ||
|---|---|---|
| 24 | 24 |
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase; |
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
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import eu.etaxonomy.cdm.io.common.Source; |
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import eu.etaxonomy.cdm.io.common.TdwgAreaProvider; |
|
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import eu.etaxonomy.cdm.model.agent.Team; |
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary; |
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import eu.etaxonomy.cdm.model.common.TermType; |
|
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import eu.etaxonomy.cdm.model.common.TimePeriod; |
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import eu.etaxonomy.cdm.model.description.DescriptionBase; |
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import eu.etaxonomy.cdm.model.description.Feature; |
| ... | ... | |
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import eu.etaxonomy.cdm.model.location.NamedArea; |
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import eu.etaxonomy.cdm.model.location.Point; |
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import eu.etaxonomy.cdm.model.location.ReferenceSystem; |
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import eu.etaxonomy.cdm.model.location.TdwgArea; |
|
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import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry; |
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import eu.etaxonomy.cdm.model.location.Country; |
|
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import eu.etaxonomy.cdm.model.occurrence.Collection; |
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType; |
|
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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|
| ... | ... | |
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TransactionStatus txStatus = this.startTransaction(); |
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|
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boolean isOrdered = true; |
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OrderedTermVocabulary<State> climateVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraClimate, "Climate", "Climate", abbrevLabel, uri, isOrdered, null); |
|
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OrderedTermVocabulary<State> habitatVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraHabitat, "Habitat", "Habitat", abbrevLabel, uri, isOrdered, null); |
|
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OrderedTermVocabulary<State> lifeformVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraLifeForm, "Lifeform", "Lifeform", abbrevLabel, uri, isOrdered, null); |
|
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OrderedTermVocabulary<State> climateVoc = (OrderedTermVocabulary)getVocabulary(TermType.State, uuidVocAlgaTerraClimate, "Climate", "Climate", abbrevLabel, uri, isOrdered, null);
|
|
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OrderedTermVocabulary<State> habitatVoc = (OrderedTermVocabulary)getVocabulary(TermType.State, uuidVocAlgaTerraHabitat, "Habitat", "Habitat", abbrevLabel, uri, isOrdered, null);
|
|
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OrderedTermVocabulary<State> lifeformVoc = (OrderedTermVocabulary)getVocabulary(TermType.State, uuidVocAlgaTerraLifeForm, "Lifeform", "Lifeform", abbrevLabel, uri, isOrdered, null);
|
|
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|
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|
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Feature feature = getFeature(state, uuidFeatureAlgaTerraClimate, "Climate","Climate", null, null); |
| ... | ... | |
| 174 | 176 |
String geoCodeMethod = rs.getString("GeoCodeMethod");
|
| 175 | 177 |
|
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Integer altitude = nullSafeInt(rs, "Altitude"); |
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Integer lowerAltitude = nullSafeInt(rs,"AltitudeLowerValue"); |
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Integer lowerAltitude = nullSafeInt(rs, "AltitudeLowerValue");
|
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String altitudeUnit = rs.getString("AltitudeUnit");
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Double depth = nullSafeDouble(rs, "Depth"); |
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Double depthLow = nullSafeDouble(rs, "DepthLow"); |
| ... | ... | |
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if (lowerAltitude == null){
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facade.setAbsoluteElevation(altitude); |
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}else{
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if (! facade.isEvenDistance(lowerAltitude, altitude)){
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//FIXME there is a ticket for this |
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altitude = altitude + 1; |
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logger.info("Current implementation of altitude does not allow uneven distances");
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} |
|
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facade.setAbsoluteElevationRange(lowerAltitude,altitude); |
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} |
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} |
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if ( depth != null){
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//FIXME needs model change to accept double #3072 |
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Integer intDepth = depth.intValue(); |
|
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if (depthLow == null){
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facade.setDistanceToWaterSurface(intDepth);
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facade.setDistanceToWaterSurface(depth);
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}else{
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//FIXME range not yet in model #3074
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facade.setDistanceToWaterSurface(intDepth);
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//TODO which direction is correct?
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facade.setDistanceToWaterSurfaceRange(depth, depthLow);
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} |
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} |
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|
| ... | ... | |
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|
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//id, created, updated, notes |
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if (unitId != null){
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this.doIdCreatedUpdatedNotes(state, facade.innerFieldObservation(), rs, unitId, getFieldObservationNameSpace());
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this.doIdCreatedUpdatedNotes(state, facade.innerFieldUnit(), rs, unitId, getFieldObservationNameSpace());
|
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}else{
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logger.warn("FieldObservation has no unitId: " + facade.innerFieldObservation() + ": " + getFieldObservationNameSpace());
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logger.warn("FieldObservation has no unitId: " + facade.innerFieldUnit() + ": " + getFieldObservationNameSpace());
|
|
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} |
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} catch (Exception e) {
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throw new RuntimeException(e); |
| ... | ... | |
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|
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|
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protected DescriptionBase getFieldObservationDescription(DerivedUnitFacade facade) {
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Set<DescriptionBase> descriptions = facade.innerFieldObservation().getDescriptions();
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Set<DescriptionBase> descriptions = facade.innerFieldUnit().getDescriptions();
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for (DescriptionBase desc : descriptions){
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if (desc.isImageGallery() == false){
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return desc; |
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} |
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} |
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SpecimenDescription specDesc = SpecimenDescription.NewInstance(facade.innerFieldObservation());
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SpecimenDescription specDesc = SpecimenDescription.NewInstance(facade.innerFieldUnit());
|
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descriptions.add(specDesc); |
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return specDesc; |
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} |
| ... | ... | |
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NamedArea tdwgArea; |
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String tdwg4 = rs.getString("L4Code");
|
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if (isNotBlank(tdwg4)){
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tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg4); |
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tdwgArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwg4);
|
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}else{
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String tdwg3 = rs.getString("L3Code");
|
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if (isNotBlank(tdwg3)){
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tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg3); |
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tdwgArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwg3);
|
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}else{
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Integer tdwg2 = rs.getInt("L2Code");
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tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(String.valueOf(tdwg2)); |
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tdwgArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(String.valueOf(tdwg2));
|
|
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} |
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} |
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if (tdwgArea == null){
|
| ... | ... | |
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} |
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|
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//Countries |
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WaterbodyOrCountry country = null;
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Country country = null; |
|
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String isoCountry = rs.getString("ISOCountry");
|
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String countryStr = rs.getString("Country");
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if (isNotBlank(isoCountry)){
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country = WaterbodyOrCountry.getWaterbodyOrCountryByIso3166A2(isoCountry);
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country = Country.getCountryByIso3166A2(isoCountry);
|
|
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}else if (isNotBlank(countryStr)){
|
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logger.warn("Country exists but no ISO code");
|
| 322 | 317 |
} |
| ... | ... | |
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} |
| 330 | 325 |
|
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//Waterbody |
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WaterbodyOrCountry waterbody = null;
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NamedArea waterbody = null;
|
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String waterbodyStr = rs.getString("WaterBody");
|
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if (isNotBlank(waterbodyStr)){
|
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if (waterbodyStr.equals("Atlantic Ocean")){
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waterbody = WaterbodyOrCountry.ATLANTICOCEAN();
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waterbody = NamedArea.ATLANTICOCEAN();
|
|
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}else{
|
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logger.warn("Waterbody not recognized: " + waterbody);
|
| 339 | 334 |
} |
| ... | ... | |
| 348 | 343 |
} |
| 349 | 344 |
|
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|
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protected SpecimenOrObservationType makeDerivedUnitType(String recordBasis) {
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SpecimenOrObservationType result = null; |
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if (StringUtils.isBlank(recordBasis)){
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result = SpecimenOrObservationType.DerivedUnit; |
|
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} else if (recordBasis.equalsIgnoreCase("FossileSpecimen")){
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result = SpecimenOrObservationType.Fossil; |
|
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}else if (recordBasis.equalsIgnoreCase("HumanObservation")){
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result = SpecimenOrObservationType.HumanObservation; |
|
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}else if (recordBasis.equalsIgnoreCase("Literature")){
|
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//FIXME |
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logger.warn("Literature record basis not yet supported");
|
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result = SpecimenOrObservationType.DerivedUnit; |
|
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}else if (recordBasis.equalsIgnoreCase("LivingSpecimen")){
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result = SpecimenOrObservationType.LivingSpecimen; |
|
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}else if (recordBasis.equalsIgnoreCase("MachineObservation")){
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result = SpecimenOrObservationType.MachineObservation; |
|
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}else if (recordBasis.equalsIgnoreCase("Observation")){
|
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result = SpecimenOrObservationType.Observation; |
|
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}else if (recordBasis.equalsIgnoreCase("LivingCulture")){
|
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//FIXME |
|
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logger.warn("LivingCulture record basis not yet supported");
|
|
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result = SpecimenOrObservationType.DerivedUnit; |
|
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}else if (recordBasis.equalsIgnoreCase("PreservedSpecimen")){
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result = SpecimenOrObservationType.PreservedSpecimen; |
|
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} |
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return result; |
|
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} |
|
| 352 | 373 |
|
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|
|
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protected Feature makeFeature(SpecimenOrObservationType type) {
|
|
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if (type.equals(SpecimenOrObservationType.DerivedUnit)){
|
|
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return Feature.INDIVIDUALS_ASSOCIATION(); |
|
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}else if (type.isFeatureObservation()){
|
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return Feature.OBSERVATION(); |
|
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}else if (type.isPreservedSpecimen()){
|
|
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return Feature.SPECIMEN(); |
|
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} |
|
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logger.warn("No feature defined for derived unit type: " + type);
|
|
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return null; |
|
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} |
|
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|
|
| 353 | 387 |
private ReferenceSystem makeRefrenceSystem(String geoCodeMethod, AlgaTerraImportState state) {
|
| 354 | 388 |
if (StringUtils.isBlank(geoCodeMethod)){
|
| 355 | 389 |
return null; |
Also available in: Unified diff
reintegrate cdmlib-app-3.3 branch into trunk