Package org.gbif.api.model.occurrence

Class Occurrence

java.lang.Object

org.gbif.api.model.occurrence.VerbatimOccurrence

org.gbif.api.model.occurrence.Occurrence

All Implemented Interfaces:

LinneanClassification, LinneanClassificationKeys

public class Occurrence
extends VerbatimOccurrence
implements LinneanClassification, LinneanClassificationKeys

Represents an Occurrence as interpreted by GBIF, adding typed properties on top of the verbatim ones.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	GEO_DATUM

Constructor Summary

Constructors

Constructor	Description
Occurrence()
Occurrence(VerbatimOccurrence verbatim)	Create occurrence instance from existing verbatim one, copying over all data.

Method Summary

Modifier and Type	Method	Description
void	addIssue(OccurrenceIssue issue)
String	getAcceptedScientificName()	The accepted scientific name for the acceptedTaxonKey from the GBIF backbone.
Integer	getAcceptedTaxonKey()	The accepted taxon key from the GBIF backbone.
String	getAssociatedSequences()	A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the material entity.
BasisOfRecord	getBasisOfRecord()
String	getBed()
Integer	getClassKey()	Return the class key for this usage.
String	getClazz()	Return the class for this usage.
@Experimental String	getCollectionKey()
Continent	getContinent()
Double	getCoordinateAccuracy()	Deprecated. to be removed in the public v2 of the API (see POR-3061) The uncertainty for latitude in decimal degrees.
Double	getCoordinatePrecision()
Double	getCoordinateUncertaintyInMeters()	The uncertainty radius for lat/lon in meters.
Country	getCountry()
String	getDatasetID()
String	getDatasetName()
Date	getDateIdentified()
@Min(1L) @Max(31L) Integer	getDay()	The day of the month of the event date.
Double	getDecimalLatitude()
Double	getDecimalLongitude()	The decimalLongitude in decimal degrees always for the WGS84 datum.
String	getDegreeOfEstablishment()
Double	getDepth()	Depth in meters below the surface.
Double	getDepthAccuracy()	Depth accuracy is the uncertainty for the depth in meters.
Double	getDistanceFromCentroidInMeters()	The distance in metres from a known centroid, e.g.
List<String>	getDnaSequenceID()
String	getEarliestAgeOrLowestStage()
String	getEarliestEonOrLowestEonothem()
String	getEarliestEpochOrLowestSeries()
String	getEarliestEraOrLowestErathem()
String	getEarliestPeriodOrLowestSystem()
Double	getElevation()	Elevation in meters usually above sea level (altitude).
Double	getElevationAccuracy()	Elevation accuracy is the uncertainty for the elevation in meters.
@Min(1L) @Max(366L) Integer	getEndDayOfYear()	The latest integer day of the year of the event.
String	getEstablishmentMeans()
IsoDateInterval	getEventDate()	The date the occurrence was recorded or collected.
@NotNull List<MeasurementOrFact>	getFacts()
String	getFamily()	Return the family for this usage.
Integer	getFamilyKey()	Return the family key for this usage.
String	getFormation()
@NotNull Gadm	getGadm()
GbifRegion	getGbifRegion()
String	getGenericName()
String	getGenus()	Return the genus for this usage.
Integer	getGenusKey()	Return the genus key for this usage.
String	getGeodeticDatum()	The geodetic datum for the interpreted decimal coordinates.
String	getGeoreferencedBy()
String	getGroup()
@NotNull Map<Integer,String>	getHigherClassificationMap()	An ordered map with entries for all higher Linnean ranks excluding the taxonKey itself.
String	getHigherGeography()
String	getHigherRank(Rank rank)	Gets a higher taxon property by passing the rank of it.
Integer	getHigherRankKey(Rank rank)	Gets a higher taxon key by passing the rank of it.
String	getHighestBiostratigraphicZone()
String	getIdentifiedBy()
@NotNull List<AgentIdentifier>	getIdentifiedByIds()
@NotNull List<Identifier>	getIdentifiers()
Integer	getIndividualCount()
String	getInfraspecificEpithet()
@Experimental String	getInstitutionKey()
boolean	getIsInCluster()
boolean	getIsSequenced()	Flag occurrence when associatedSequences/extension exists
@NotNull Set<OccurrenceIssue>	getIssues()	A set of issues found for this occurrence.
String	getIucnRedListCategory()	The IUCN Red List Category.
String	getKingdom()	Return the kingdom for this usage.
Integer	getKingdomKey()	Return the kingdom key for this usage.
Date	getLastInterpreted()	The date this occurrence last went through the interpretation phase of the GBIF indexing.
String	getLatestAgeOrHighestStage()
String	getLatestEonOrHighestEonothem()
String	getLatestEpochOrHighestSeries()
String	getLatestEraOrHighestErathem()
String	getLatestPeriodOrHighestSystem()
@NotNull License	getLicense()	Applied license to the occurrence record or dataset to which this record belongs to.
String	getLifeStage()
String	getLowestBiostratigraphicZone()
@NotNull List<MediaObject>	getMedia()
String	getMember()
Date	getModified()	The interpreted dc:modified from the verbatim source data.
@Min(1L) @Max(12L) Integer	getMonth()	The month of the year of the event date starting with zero for january following Date.
OccurrenceStatus	getOccurrenceStatus()
String	getOrder()	Return the order for this usage.
Integer	getOrderKey()	Return the order key for this usage.
Double	getOrganismQuantity()	A number or enumeration value for the quantity of organisms.
String	getOrganismQuantityType()	The type of quantification system used for the quantity of organisms.
String	getOtherCatalogNumbers()
String	getPathway()
String	getPhylum()	Return the phylum for this usage.
Integer	getPhylumKey()	Return the phylum key for this usage.
String	getPreparations()
String	getRecordedBy()
@NotNull List<AgentIdentifier>	getRecordedByIds()
URI	getReferences()	An external link to more details, the records "homepage".
@NotNull List<OccurrenceRelation>	getRelations()
Double	getRelativeOrganismQuantity()	Calculated filed organismQuantity / sampleSizeValue, if the type is identical
String	getSampleSizeUnit()	The unit of measurement of the size (time duration, length, area, or volume) of a sample in a sampling event.
Double	getSampleSizeValue()	A numeric value for a measurement of the size (time duration, length, area, or volume) of a sample in a sampling event.
String	getSamplingProtocol()
String	getScientificName()	The scientific name for taxonKey from the GBIF backbone.
String	getSex()
String	getSpecies()	The corresponding scientific name of the speciesKey from the GBIF backbone.
Integer	getSpeciesKey()	The accepted species for this occurrence.
String	getSpecificEpithet()
@Min(1L) @Max(366L) Integer	getStartDayOfYear()	The earliest integer day of the year of the event.
String	getStateProvince()
String	getSubgenus()	Return the canonical subgenus name for this usage.
Integer	getSubgenusKey()	Return the subgenus key for this usage.
Integer	getTaxonKey()	The best matching, accepted GBIF backbone name usage representing this occurrence.
TaxonomicStatus	getTaxonomicStatus()	The status of the use of the scientificName as a label for a taxon.
Rank	getTaxonRank()
String	getTypeStatus()
String	getTypifiedName()	The scientific name the type status of this specimen applies to.
String	getVerbatimScientificName()	The verbatim scientific name as provided by the source.
String	getWaterBody()
@Min(1500L) @Max(2030L) Integer	getYear()	The full year of the event date.
boolean	hasSpatialIssue()	Convenience method checking if any spatial validation rule has not passed.
void	setAcceptedScientificName(String acceptedScientificName)
void	setAcceptedTaxonKey(Integer acceptedTaxonKey)
void	setAssociatedSequences(String associatedSequences)
void	setBasisOfRecord(BasisOfRecord basisOfRecord)
void	setBed(String bed)
void	setClassKey(Integer classKey)
void	setClazz(String clazz)
void	setCollectionKey(String collectionKey)
void	setContinent(Continent continent)
void	setCoordinateAccuracy(Double coordinateAccuracy)
void	setCoordinatePrecision(Double coordinatePrecision)
void	setCoordinateUncertaintyInMeters(Double coordinateUncertaintyInMeters)
void	setCountry(Country country)
void	setDatasetID(String datasetID)
void	setDatasetName(String datasetName)
void	setDateIdentified(Date dateIdentified)
void	setDay(Integer day)
void	setDecimalLatitude(Double decimalLatitude)
void	setDecimalLongitude(Double decimalLongitude)
void	setDegreeOfEstablishment(String degreeOfEstablishment)
void	setDepth(Double depth)
void	setDepthAccuracy(Double depthAccuracy)
void	setDistanceFromCentroidInMeters(Double distanceFromCentroidInMeters)
void	setDnaSequenceID(List<String> dnaSequenceID)
void	setEarliestAgeOrLowestStage(String earliestAgeOrLowestStage)
void	setEarliestEonOrLowestEonothem(String earliestEonOrLowestEonothem)
void	setEarliestEpochOrLowestSeries(String earliestEpochOrLowestSeries)
void	setEarliestEraOrLowestErathem(String earliestEraOrLowestErathem)
void	setEarliestPeriodOrLowestSystem(String earliestPeriodOrLowestSystem)
void	setElevation(Double elevation)
void	setElevationAccuracy(Double elevationAccuracy)
void	setEndDayOfYear(Integer endDayOfYear)
void	setEstablishmentMeans(String establishmentMeans)
void	setEventDate(IsoDateInterval eventDate)
void	setFacts(List<MeasurementOrFact> facts)
void	setFamily(String family)
void	setFamilyKey(Integer familyKey)
void	setFormation(String formation)
void	setGadm(Gadm gadm)
void	setGenericName(String genericName)
void	setGenus(String genus)
void	setGenusKey(Integer genusKey)
void	setGeoreferencedBy(String georeferencedBy)
void	setGroup(String group)
void	setHigherGeography(String higherGeography)
void	setHighestBiostratigraphicZone(String highestBiostratigraphicZone)
void	setIdentifiedBy(String identifiedBy)
void	setIdentifiedByIds(List<AgentIdentifier> identifiedByIds)
void	setIdentifiers(List<Identifier> identifiers)
void	setIndividualCount(Integer individualCount)
void	setInfraspecificEpithet(String infraspecificEpithet)
void	setInstitutionKey(String institutionKey)
void	setIsInCluster(boolean isInCluster)
void	setIsSequenced(boolean isSequenced)
void	setIssues(Set<OccurrenceIssue> issues)
void	setIucnRedListCategory(String iucnRedListCategory)
void	setKingdom(String kingdom)
void	setKingdomKey(Integer kingdomKey)
void	setLastInterpreted(Date lastInterpreted)
void	setLatestAgeOrHighestStage(String latestAgeOrHighestStage)
void	setLatestEonOrHighestEonothem(String latestEonOrHighestEonothem)
void	setLatestEpochOrHighestSeries(String latestEpochOrHighestSeries)
void	setLatestEraOrHighestErathem(String latestEraOrHighestErathem)
void	setLatestPeriodOrHighestSystem(String latestPeriodOrHighestSystem)
void	setLicense(License license)
void	setLifeStage(String lifeStage)
void	setLowestBiostratigraphicZone(String lowestBiostratigraphicZone)
void	setMedia(List<MediaObject> media)
void	setMember(String member)
void	setModified(Date modified)
void	setMonth(Integer month)
void	setOccurrenceStatus(OccurrenceStatus occurrenceStatus)
void	setOrder(String order)
void	setOrderKey(Integer orderKey)
void	setOrganismQuantity(Double organismQuantity)
void	setOrganismQuantityType(String organismQuantityType)
void	setOtherCatalogNumbers(String otherCatalogNumbers)
void	setPathway(String pathway)
void	setPhylum(String phylum)
void	setPhylumKey(Integer phylumKey)
void	setPreparations(String preparations)
void	setRecordedBy(String recordedBy)
void	setRecordedByIds(List<AgentIdentifier> recordedByIds)
void	setReferences(URI references)
void	setRelations(List<OccurrenceRelation> relations)
void	setRelativeOrganismQuantity(Double relativeOrganismQuantity)
void	setSampleSizeUnit(String sampleSizeUnit)
void	setSampleSizeValue(Double sampleSizeValue)
void	setSamplingProtocol(String samplingProtocol)
void	setScientificName(String scientificName)
void	setSex(String sex)
void	setSpecies(String species)
void	setSpeciesKey(Integer speciesKey)
void	setSpecificEpithet(String specificEpithet)
void	setStartDayOfYear(Integer startDayOfYear)
void	setStateProvince(String stateProvince)
void	setSubgenus(String subgenus)
void	setSubgenusKey(Integer subgenusKey)
void	setTaxonKey(Integer taxonKey)
void	setTaxonomicStatus(TaxonomicStatus taxonomicStatus)
void	setTaxonRank(Rank taxonRank)
void	setTypeStatus(String typeStatus)
void	setTypifiedName(String typifiedName)
void	setVerbatimScientificName(String scientificName)
void	setWaterBody(String waterBody)
void	setYear(Integer year)

Methods inherited from class org.gbif.api.model.occurrence.VerbatimOccurrence

equals, getCrawlId, getDatasetKey, getExtensions, getHostingOrganizationKey, getInstallationKey, getKey, getLastCrawled, getLastParsed, getNetworkKeys, getProgrammeAcronym, getProjectId, getProtocol, getPublishedByGbifRegion, getPublishingCountry, getPublishingOrgKey, getVerbatimField, getVerbatimFields, hashCode, hasVerbatimField, setCrawlId, setDatasetKey, setExtensions, setHostingOrganizationKey, setInstallationKey, setKey, setLastCrawled, setLastParsed, setNetworkKeys, setProgrammeAcronym, setProjectId, setProtocol, setPublishedByGbifRegion, setPublishingCountry, setPublishingOrgKey, setVerbatimField, setVerbatimFields, toString

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Field Details

GEO_DATUM

public static final String GEO_DATUM

See Also:

• Constant Field Values

Constructor Details

Occurrence

public Occurrence()

Occurrence

public Occurrence(@Nullable
 VerbatimOccurrence verbatim)

Create occurrence instance from existing verbatim one, copying over all data.

Method Details

getBasisOfRecord

@Nullable
public BasisOfRecord getBasisOfRecord()

setBasisOfRecord

public void setBasisOfRecord(BasisOfRecord basisOfRecord)

getIndividualCount

@Nullable
public Integer getIndividualCount()

setIndividualCount

public void setIndividualCount(Integer individualCount)

getOccurrenceStatus

@Nullable
public OccurrenceStatus getOccurrenceStatus()

setOccurrenceStatus

public void setOccurrenceStatus(OccurrenceStatus occurrenceStatus)

getSex

@Nullable
public String getSex()

setSex

public void setSex(String sex)

getLifeStage

@Nullable
public String getLifeStage()

setLifeStage

public void setLifeStage(String lifeStage)

getEstablishmentMeans

@Nullable
public String getEstablishmentMeans()

setEstablishmentMeans

public void setEstablishmentMeans(String establishmentMeans)

getTaxonKey

@Nullable
public Integer getTaxonKey()

The best matching, accepted GBIF backbone name usage representing this occurrence. In case the verbatim scientific name and its classification can only be matched to a higher rank this will represent the lowest matching rank. In the worst case this could just be for example Animalia.

setTaxonKey

public void setTaxonKey(Integer taxonKey)

getKingdomKey

@Nullable
public Integer getKingdomKey()

Description copied from interface: LinneanClassificationKeys

Return the kingdom key for this usage. If the usage is for something above the "kingdom" taxonomic level, return null.

Specified by:

getKingdomKey in interface LinneanClassificationKeys

Returns:

the kingdomKey

setKingdomKey

public void setKingdomKey(@Nullable
 Integer kingdomKey)

Specified by:

setKingdomKey in interface LinneanClassificationKeys

Parameters:

kingdomKey - the kingdomKey to set

getPhylumKey

@Nullable
public Integer getPhylumKey()

Description copied from interface: LinneanClassificationKeys

Return the phylum key for this usage. If the usage is for something above the "phylum" taxonomic level, return null.

Specified by:

getPhylumKey in interface LinneanClassificationKeys

Returns:

the phylumKey

setPhylumKey

public void setPhylumKey(@Nullable
 Integer phylumKey)

Specified by:

setPhylumKey in interface LinneanClassificationKeys

Parameters:

phylumKey - the phylumKey to set

getClassKey

@Nullable
public Integer getClassKey()

Description copied from interface: LinneanClassificationKeys

Return the class key for this usage. If the usage is for something above the "class" taxonomic level, return null.

Specified by:

getClassKey in interface LinneanClassificationKeys

Returns:

the classKey

setClassKey

public void setClassKey(@Nullable
 Integer classKey)

Specified by:

setClassKey in interface LinneanClassificationKeys

Parameters:

classKey - the classKey to set

getOrderKey

@Nullable
public Integer getOrderKey()

Description copied from interface: LinneanClassificationKeys

Return the order key for this usage. If the usage is for something above the "order" taxonomic level, return null.

Specified by:

getOrderKey in interface LinneanClassificationKeys

Returns:

the orderKey

setOrderKey

public void setOrderKey(@Nullable
 Integer orderKey)

Specified by:

setOrderKey in interface LinneanClassificationKeys

Parameters:

orderKey - the orderKey to set

getFamilyKey

@Nullable
public Integer getFamilyKey()

Description copied from interface: LinneanClassificationKeys

Return the family key for this usage. If the usage is for something above the "family" taxonomic level, return null.

Specified by:

getFamilyKey in interface LinneanClassificationKeys

Returns:

the familyKey

setFamilyKey

public void setFamilyKey(@Nullable
 Integer familyKey)

Specified by:

setFamilyKey in interface LinneanClassificationKeys

Parameters:

familyKey - the familyKey to set

getGenusKey

@Nullable
public Integer getGenusKey()

Description copied from interface: LinneanClassificationKeys

Return the genus key for this usage. If the usage is for something above the "genus" taxonomic level, return null.

Specified by:

getGenusKey in interface LinneanClassificationKeys

Returns:

the genusKey

setGenusKey

public void setGenusKey(@Nullable
 Integer genusKey)

Specified by:

setGenusKey in interface LinneanClassificationKeys

Parameters:

genusKey - the genusKey to set

getSubgenusKey

@Nullable
public Integer getSubgenusKey()

Description copied from interface: LinneanClassificationKeys

Return the subgenus key for this usage. If the usage is for something above the "subgenus" taxonomic level, return null.

Specified by:

getSubgenusKey in interface LinneanClassificationKeys

Returns:

subgenusKey

setSubgenusKey

public void setSubgenusKey(@Nullable
 Integer subgenusKey)

Specified by:

setSubgenusKey in interface LinneanClassificationKeys

Parameters:

subgenusKey - the subgenus usage key

getHigherRankKey

@Nullable
public Integer getHigherRankKey(Rank rank)

Description copied from interface: LinneanClassificationKeys

Gets a higher taxon key by passing the rank of it. Only Linnean ranks are supported.

Specified by:

getHigherRankKey in interface LinneanClassificationKeys

Parameters:

rank - the higher linnean rank to retrieve

Returns:

the key of the higher taxon or null if rank doesnt exist

getHigherClassificationMap

@NotNull
public @NotNull Map<Integer,String> getHigherClassificationMap()

An ordered map with entries for all higher Linnean ranks excluding the taxonKey itself. The map starts with the highest rank, e.g. the kingdom and maps the name usage key to its canonical name.

Returns:

map of higher ranks

getSpeciesKey

@Nullable
public Integer getSpeciesKey()

The accepted species for this occurrence. In case the taxonKey is of a higher rank than species (e.g. genus) speciesKey is null. In case taxonKey represents an infraspecific taxon the speciesKey points to the species the infraspecies is classified as. In case of taxonKey being a species the speciesKey is the same.

Specified by:

getSpeciesKey in interface LinneanClassificationKeys

Returns:

the speciesKey

setSpeciesKey

public void setSpeciesKey(@Nullable
 Integer speciesKey)

Specified by:

setSpeciesKey in interface LinneanClassificationKeys

Parameters:

speciesKey - the speciesKey to set

getAcceptedTaxonKey

@Nullable
public Integer getAcceptedTaxonKey()

The accepted taxon key from the GBIF backbone.

setAcceptedTaxonKey

public void setAcceptedTaxonKey(Integer acceptedTaxonKey)

getSpecificEpithet

@Nullable
public String getSpecificEpithet()

setSpecificEpithet

public void setSpecificEpithet(String specificEpithet)

getInfraspecificEpithet

@Nullable
public String getInfraspecificEpithet()

setInfraspecificEpithet

public void setInfraspecificEpithet(String infraspecificEpithet)

getTaxonRank

@Nullable
public Rank getTaxonRank()

setTaxonRank

public void setTaxonRank(Rank taxonRank)

getTaxonomicStatus

@Nullable
public TaxonomicStatus getTaxonomicStatus()

The status of the use of the scientificName as a label for a taxon. The GBIF recommended controlled value vocabulary can be found at http://rs.gbif.org/vocabulary/gbif/taxonomic_status.xm.

setTaxonomicStatus

public void setTaxonomicStatus(TaxonomicStatus taxonomicStatus)

getIucnRedListCategory

@Nullable
public String getIucnRedListCategory()

The IUCN Red List Category.

setIucnRedListCategory

public void setIucnRedListCategory(String iucnRedListCategory)

getScientificName

@Nullable
public String getScientificName()

The scientific name for taxonKey from the GBIF backbone.

setScientificName

public void setScientificName(@Nullable
 String scientificName)

getVerbatimScientificName

@Nullable
public String getVerbatimScientificName()

The verbatim scientific name as provided by the source.

setVerbatimScientificName

public void setVerbatimScientificName(String scientificName)

getAcceptedScientificName

@Nullable
public String getAcceptedScientificName()

The accepted scientific name for the acceptedTaxonKey from the GBIF backbone.

setAcceptedScientificName

public void setAcceptedScientificName(String acceptedScientificName)

getKingdom

@Nullable
public String getKingdom()

Description copied from interface: LinneanClassification

Return the kingdom for this usage. If the usage is for something above the "kingdom" taxonomic level, return null.

Specified by:

getKingdom in interface LinneanClassification

Returns:

the kingdom

setKingdom

public void setKingdom(@Nullable
 String kingdom)

Specified by:

setKingdom in interface LinneanClassification

Parameters:

kingdom - the kingdom to set

getPhylum

@Nullable
public String getPhylum()

Description copied from interface: LinneanClassification

Return the phylum for this usage. If the usage is for something above the "phylum" taxonomic level, return null.

Specified by:

getPhylum in interface LinneanClassification

Returns:

the phylum

setPhylum

public void setPhylum(@Nullable
 String phylum)

Specified by:

setPhylum in interface LinneanClassification

Parameters:

phylum - the phylum to set

getClazz

@Nullable
public String getClazz()

Description copied from interface: LinneanClassification

Return the class for this usage. If the usage is for something above the "class" taxonomic level, return null.

Specified by:

getClazz in interface LinneanClassification

Returns:

the class

setClazz

public void setClazz(@Nullable
 String clazz)

Specified by:

setClazz in interface LinneanClassification

Parameters:

clazz - the clazz to set

getOrder

@Nullable
public String getOrder()

Description copied from interface: LinneanClassification

Return the order for this usage. If the usage is for something above the "order" taxonomic level, return null.

Specified by:

getOrder in interface LinneanClassification

Returns:

the order

setOrder

public void setOrder(@Nullable
 String order)

Specified by:

setOrder in interface LinneanClassification

Parameters:

order - the order to set

getFamily

@Nullable
public String getFamily()

Description copied from interface: LinneanClassification

Return the family for this usage. If the usage is for something above the "family" taxonomic level, return null.

Specified by:

getFamily in interface LinneanClassification

Returns:

the family

setFamily

public void setFamily(@Nullable
 String family)

Specified by:

setFamily in interface LinneanClassification

Parameters:

family - the family to set

getGenus

@Nullable
public String getGenus()

Description copied from interface: LinneanClassification

Return the genus for this usage. If the usage is for something above the "genus" taxonomic level, return null.

Specified by:

getGenus in interface LinneanClassification

Returns:

the genus

setGenus

public void setGenus(@Nullable
 String genus)

Specified by:

setGenus in interface LinneanClassification

Parameters:

genus - the genus to set

getGenericName

@Nullable
public String getGenericName()

setGenericName

public void setGenericName(String genericName)

getSubgenus

@Nullable
public String getSubgenus()

Description copied from interface: LinneanClassification

Return the canonical subgenus name for this usage. If the usage is for something above the "subgenus" taxonomic level, return null.

Specified by:

getSubgenus in interface LinneanClassification

Returns:

the subgenus name

setSubgenus

public void setSubgenus(@Nullable
 String subgenus)

Specified by:

setSubgenus in interface LinneanClassification

Parameters:

subgenus - the subgenus canonical name

getHigherRank

@Nullable
public String getHigherRank(Rank rank)

Description copied from interface: LinneanClassification

Gets a higher taxon property by passing the rank of it. Only Linnean ranks are supported.

Specified by:

getHigherRank in interface LinneanClassification

Parameters:

rank - the higher linnean rank to retrieve

Returns:

the name of the higher taxon or null if rank doesnt exist

getSpecies

@Nullable
public String getSpecies()

The corresponding scientific name of the speciesKey from the GBIF backbone.

Specified by:

getSpecies in interface LinneanClassification

Returns:

the species

setSpecies

public void setSpecies(@Nullable
 String species)

Specified by:

setSpecies in interface LinneanClassification

Parameters:

species - the species to set

getDateIdentified

@Nullable
public Date getDateIdentified()

setDateIdentified

public void setDateIdentified(@Nullable
 Date dateIdentified)

getDecimalLongitude

@Nullable
public Double getDecimalLongitude()

The decimalLongitude in decimal degrees always for the WGS84 datum. If a different geodetic datum was given the verbatim coordinates are transformed into WGS84 values.

setDecimalLongitude

public void setDecimalLongitude(@Nullable
 Double decimalLongitude)

getDecimalLatitude

@Nullable
public Double getDecimalLatitude()

setDecimalLatitude

public void setDecimalLatitude(@Nullable
 Double decimalLatitude)

getCoordinateUncertaintyInMeters

@Nullable
public Double getCoordinateUncertaintyInMeters()

The uncertainty radius for lat/lon in meters.

setCoordinateUncertaintyInMeters

public void setCoordinateUncertaintyInMeters(@Nullable
 Double coordinateUncertaintyInMeters)

getCoordinatePrecision

@Nullable
public Double getCoordinatePrecision()

setCoordinatePrecision

public void setCoordinatePrecision(Double coordinatePrecision)

getCoordinateAccuracy

@Nullable
@Deprecated
public Double getCoordinateAccuracy()

Deprecated.

to be removed in the public v2 of the API (see POR-3061) The uncertainty for latitude in decimal degrees. Note that the longitude degrees have a different accuracy in degrees which changes with latitude and is largest at the poles.

setCoordinateAccuracy

public void setCoordinateAccuracy(@Nullable
 Double coordinateAccuracy)

getGeodeticDatum

@Nullable
public String getGeodeticDatum()

The geodetic datum for the interpreted decimal coordinates. This is always WGS84 if a coordinate exists as we reproject other datums into WGS84.

getElevation

@Nullable
public Double getElevation()

Elevation in meters usually above sea level (altitude).
The elevation is calculated using the equation: (minimumElevationInMeters + maximumElevationInMeters) / 2.

setElevation

public void setElevation(@Nullable
 Double elevation)

getElevationAccuracy

@Nullable
public Double getElevationAccuracy()

Elevation accuracy is the uncertainty for the elevation in meters.
The elevation accuracy is calculated using the equation: (maximumElevationInMeters - minimumElevationInMeters) / 2

setElevationAccuracy

public void setElevationAccuracy(@Nullable
 Double elevationAccuracy)

getDepth

@Nullable
public Double getDepth()

Depth in meters below the surface. Complimentary to elevation, the depth can be 10 meters below the surface of a lake in 1100m (=elevation).
The depth is calculated using the equation: (minimumDepthInMeters + maximumDepthInMeters) / 2.

setDepth

public void setDepth(@Nullable
 Double depth)

getDepthAccuracy

@Nullable
public Double getDepthAccuracy()

Depth accuracy is the uncertainty for the depth in meters.
The depth accuracy is calculated using the equation: (maximumDepthInMeters - minimumDepthInMeters) / 2

setDepthAccuracy

public void setDepthAccuracy(@Nullable
 Double depthAccuracy)

getContinent

@Nullable
public Continent getContinent()

setContinent

public void setContinent(@Nullable
 Continent continent)

getCountry

@Nullable
public Country getCountry()

setCountry

public void setCountry(@Nullable
 Country country)

getGbifRegion

@Nullable
public GbifRegion getGbifRegion()

getStateProvince

@Nullable
public String getStateProvince()

setStateProvince

public void setStateProvince(@Nullable
 String stateProvince)

getWaterBody

@Nullable
public String getWaterBody()

setWaterBody

public void setWaterBody(@Nullable
 String waterBody)

getDistanceFromCentroidInMeters

public Double getDistanceFromCentroidInMeters()

The distance in metres from a known centroid, e.g. a country centroid.

setDistanceFromCentroidInMeters

public void setDistanceFromCentroidInMeters(Double distanceFromCentroidInMeters)

getHigherGeography

@Nullable
public String getHigherGeography()

setHigherGeography

public void setHigherGeography(String higherGeography)

getGeoreferencedBy

@Nullable
public String getGeoreferencedBy()

setGeoreferencedBy

public void setGeoreferencedBy(String georeferencedBy)

getYear

@Min(1500L)
@Max(2030L)
@Nullable
public @Min(1500L) @Max(2030L) Integer getYear()

The full year of the event date.

Returns:

the year of the event date

setYear

public void setYear(@Nullable
 Integer year)

getMonth

@Min(1L)
@Max(12L)
@Nullable
public @Min(1L) @Max(12L) Integer getMonth()

The month of the year of the event date starting with zero for january following Date.

Returns:

the month of the event date

setMonth

public void setMonth(@Nullable
 Integer month)

getDay

@Min(1L)
@Max(31L)
@Nullable
public @Min(1L) @Max(31L) Integer getDay()

The day of the month of the event date.

Returns:

the day of the event date

setDay

public void setDay(@Nullable
 Integer day)

getEventDate

@Nullable
public IsoDateInterval getEventDate()

The date the occurrence was recorded or collected.

setEventDate

public void setEventDate(@Nullable
 IsoDateInterval eventDate)

getStartDayOfYear

@Min(1L)
@Max(366L)
@Nullable
public @Min(1L) @Max(366L) Integer getStartDayOfYear()

The earliest integer day of the year of the event.

Returns:

the earliest integer day of the event date

setStartDayOfYear

public void setStartDayOfYear(@Nullable
 Integer startDayOfYear)

getEndDayOfYear

@Min(1L)
@Max(366L)
@Nullable
public @Min(1L) @Max(366L) Integer getEndDayOfYear()

The latest integer day of the year of the event.

Returns:

the latest integer day of the event date

setEndDayOfYear

public void setEndDayOfYear(@Nullable
 Integer endDayOfYear)

getTypeStatus

@Nullable
public String getTypeStatus()

setTypeStatus

public void setTypeStatus(@Nullable
 String typeStatus)

getTypifiedName

@Nullable
public String getTypifiedName()

The scientific name the type status of this specimen applies to.

setTypifiedName

public void setTypifiedName(@Nullable
 String typifiedName)

getIssues

@NotNull
public @NotNull Set<OccurrenceIssue> getIssues()

A set of issues found for this occurrence.

setIssues

public void setIssues(Set<OccurrenceIssue> issues)

addIssue

public void addIssue(OccurrenceIssue issue)

getModified

@Nullable
public Date getModified()

The interpreted dc:modified from the verbatim source data. Ideally indicating when a record was last modified in the source.

setModified

public void setModified(@Nullable
 Date modified)

getLastInterpreted

@Nullable
public Date getLastInterpreted()

The date this occurrence last went through the interpretation phase of the GBIF indexing.

setLastInterpreted

public void setLastInterpreted(@Nullable
 Date lastInterpreted)

getReferences

@Nullable
public URI getReferences()

An external link to more details, the records "homepage".

setReferences

public void setReferences(URI references)

getOrganismQuantity

@Nullable
public Double getOrganismQuantity()

A number or enumeration value for the quantity of organisms.

setOrganismQuantity

public void setOrganismQuantity(@Nullable
 Double organismQuantity)

getOrganismQuantityType

@Nullable
public String getOrganismQuantityType()

The type of quantification system used for the quantity of organisms.

setOrganismQuantityType

public void setOrganismQuantityType(@Nullable
 String organismQuantityType)

getSampleSizeUnit

@Nullable
public String getSampleSizeUnit()

The unit of measurement of the size (time duration, length, area, or volume) of a sample in a sampling event.

setSampleSizeUnit

public void setSampleSizeUnit(@Nullable
 String sampleSizeUnit)

getSampleSizeValue

@Nullable
public Double getSampleSizeValue()

A numeric value for a measurement of the size (time duration, length, area, or volume) of a sample in a sampling event.

setSampleSizeValue

public void setSampleSizeValue(@Nullable
 Double sampleSizeValue)

getRelativeOrganismQuantity

@Nullable
public Double getRelativeOrganismQuantity()

Calculated filed organismQuantity / sampleSizeValue, if the type is identical

setRelativeOrganismQuantity

public void setRelativeOrganismQuantity(@Nullable
 Double relativeOrganismQuantity)

getIsSequenced

public boolean getIsSequenced()

Flag occurrence when associatedSequences/extension exists

setIsSequenced

public void setIsSequenced(boolean isSequenced)

getAssociatedSequences

@Nullable
public String getAssociatedSequences()

A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the material entity.

setAssociatedSequences

public void setAssociatedSequences(String associatedSequences)

getLicense

@NotNull
public @NotNull License getLicense()

Applied license to the occurrence record or dataset to which this record belongs to.

setLicense

public void setLicense(License license)

getIdentifiers

@NotNull
public @NotNull List<Identifier> getIdentifiers()

setIdentifiers

public void setIdentifiers(List<Identifier> identifiers)

getMedia

@NotNull
public @NotNull List<MediaObject> getMedia()

setMedia

public void setMedia(List<MediaObject> media)

getFacts

@NotNull
public @NotNull List<MeasurementOrFact> getFacts()

setFacts

public void setFacts(List<MeasurementOrFact> facts)

getRelations

@NotNull
public @NotNull List<OccurrenceRelation> getRelations()

setRelations

public void setRelations(List<OccurrenceRelation> relations)

getRecordedByIds

@NotNull
public @NotNull List<AgentIdentifier> getRecordedByIds()

setRecordedByIds

public void setRecordedByIds(List<AgentIdentifier> recordedByIds)

getIdentifiedByIds

@NotNull
public @NotNull List<AgentIdentifier> getIdentifiedByIds()

setIdentifiedByIds

public void setIdentifiedByIds(List<AgentIdentifier> identifiedByIds)

getGadm

@NotNull
public @NotNull Gadm getGadm()

setGadm

public void setGadm(Gadm gadm)

getInstitutionKey

@Nullable
@Experimental
public @Experimental String getInstitutionKey()

setInstitutionKey

public void setInstitutionKey(String institutionKey)

getCollectionKey

@Nullable
@Experimental
public @Experimental String getCollectionKey()

setCollectionKey

public void setCollectionKey(String collectionKey)

getIsInCluster

public boolean getIsInCluster()

setIsInCluster

public void setIsInCluster(boolean isInCluster)

getDegreeOfEstablishment

@Nullable
public String getDegreeOfEstablishment()

setDegreeOfEstablishment

public void setDegreeOfEstablishment(String degreeOfEstablishment)

getPathway

@Nullable
public String getPathway()

setPathway

public void setPathway(String pathway)

getDatasetID

public String getDatasetID()

setDatasetID

public void setDatasetID(String datasetID)

getDatasetName

public String getDatasetName()

setDatasetName

public void setDatasetName(String datasetName)

getOtherCatalogNumbers

public String getOtherCatalogNumbers()

setOtherCatalogNumbers

public void setOtherCatalogNumbers(String otherCatalogNumbers)

getEarliestEonOrLowestEonothem

@Nullable
public String getEarliestEonOrLowestEonothem()

setEarliestEonOrLowestEonothem

public void setEarliestEonOrLowestEonothem(String earliestEonOrLowestEonothem)

getLatestEonOrHighestEonothem

@Nullable
public String getLatestEonOrHighestEonothem()

setLatestEonOrHighestEonothem

public void setLatestEonOrHighestEonothem(String latestEonOrHighestEonothem)

getEarliestEraOrLowestErathem

@Nullable
public String getEarliestEraOrLowestErathem()

setEarliestEraOrLowestErathem

public void setEarliestEraOrLowestErathem(String earliestEraOrLowestErathem)

getLatestEraOrHighestErathem

@Nullable
public String getLatestEraOrHighestErathem()

setLatestEraOrHighestErathem

public void setLatestEraOrHighestErathem(String latestEraOrHighestErathem)

getEarliestPeriodOrLowestSystem

@Nullable
public String getEarliestPeriodOrLowestSystem()

setEarliestPeriodOrLowestSystem

public void setEarliestPeriodOrLowestSystem(String earliestPeriodOrLowestSystem)

getLatestPeriodOrHighestSystem

@Nullable
public String getLatestPeriodOrHighestSystem()

setLatestPeriodOrHighestSystem

public void setLatestPeriodOrHighestSystem(String latestPeriodOrHighestSystem)

getEarliestEpochOrLowestSeries

@Nullable
public String getEarliestEpochOrLowestSeries()

setEarliestEpochOrLowestSeries

public void setEarliestEpochOrLowestSeries(String earliestEpochOrLowestSeries)

getLatestEpochOrHighestSeries

@Nullable
public String getLatestEpochOrHighestSeries()

setLatestEpochOrHighestSeries

public void setLatestEpochOrHighestSeries(String latestEpochOrHighestSeries)

getEarliestAgeOrLowestStage

@Nullable
public String getEarliestAgeOrLowestStage()

setEarliestAgeOrLowestStage

public void setEarliestAgeOrLowestStage(String earliestAgeOrLowestStage)

getLatestAgeOrHighestStage

@Nullable
public String getLatestAgeOrHighestStage()

setLatestAgeOrHighestStage

public void setLatestAgeOrHighestStage(String latestAgeOrHighestStage)

getLowestBiostratigraphicZone

@Nullable
public String getLowestBiostratigraphicZone()

setLowestBiostratigraphicZone

public void setLowestBiostratigraphicZone(String lowestBiostratigraphicZone)

getHighestBiostratigraphicZone

@Nullable
public String getHighestBiostratigraphicZone()

setHighestBiostratigraphicZone

public void setHighestBiostratigraphicZone(String highestBiostratigraphicZone)

getGroup

@Nullable
public String getGroup()

setGroup

public void setGroup(String group)

getFormation

@Nullable
public String getFormation()

setFormation

public void setFormation(String formation)

getMember

@Nullable
public String getMember()

setMember

public void setMember(String member)

getBed

@Nullable
public String getBed()

setBed

public void setBed(String bed)

getRecordedBy

public String getRecordedBy()

setRecordedBy

public void setRecordedBy(String recordedBy)

getIdentifiedBy

public String getIdentifiedBy()

setIdentifiedBy

public void setIdentifiedBy(String identifiedBy)

getPreparations

public String getPreparations()

setPreparations

public void setPreparations(String preparations)

getSamplingProtocol

public String getSamplingProtocol()

setSamplingProtocol

public void setSamplingProtocol(String samplingProtocol)

getDnaSequenceID

public List<String> getDnaSequenceID()

setDnaSequenceID

public void setDnaSequenceID(List<String> dnaSequenceID)

hasSpatialIssue

public boolean hasSpatialIssue()

Convenience method checking if any spatial validation rule has not passed. Primarily used to indicate that the record should not be displayed on a map.