eu.etaxonomy.cdm.io.specimen

Class SpecimenImportConfiguratorBase<CONFIG extends SpecimenImportConfiguratorBase,STATE extends SpecimenImportStateBase<CONFIG,STATE>,InputStream>

java.lang.Object

eu.etaxonomy.cdm.io.common.ObservableBase

eu.etaxonomy.cdm.io.common.IoConfiguratorBase

eu.etaxonomy.cdm.io.common.ImportConfiguratorBase<STATE,InputStream>

eu.etaxonomy.cdm.io.specimen.SpecimenImportConfiguratorBase<CONFIG,STATE,InputStream>

All Implemented Interfaces:

IImportConfigurator, IIoConfigurator, IIoObservable, java.io.Serializable

Direct Known Subclasses:

Abcd206ImportConfigurator, GbifImportConfigurator

public abstract class SpecimenImportConfiguratorBase<CONFIG extends SpecimenImportConfiguratorBase,STATE extends SpecimenImportStateBase<CONFIG,STATE>,InputStream>
extends ImportConfiguratorBase<STATE,InputStream>

Since:

15.07.2016

Author:

k.luther

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface eu.etaxonomy.cdm.io.common.IImportConfigurator

IImportConfigurator.CHECK, IImportConfigurator.DO_REFERENCES, IImportConfigurator.EDITOR, IImportConfigurator.SOURCE_TYPE

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.Map<java.lang.String,java.util.UUID>	namedAreaDecisions
protected OccurenceQuery	query

Fields inherited from class eu.etaxonomy.cdm.io.common.ImportConfiguratorBase

ioBeans, ioClassList, ioList, sourceReference

Fields inherited from class eu.etaxonomy.cdm.io.common.IoConfiguratorBase

authenticationToken, cdmApp, hibernateConfig, INCLUDE_UNPUBLISHED, NO_UNPUBLISHED

Constructor Summary

Constructors

Constructor and Description
SpecimenImportConfiguratorBase(IInputTransformer transformer)

Method Summary

Modifier and Type	Method and Description
void	addMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen)
java.lang.String	getDefaultAuthor()
java.util.UUID	getNamedAreaDecision(java.lang.String areaStr)
java.util.Map<java.lang.String,java.util.UUID>	getNamedAreaDecisions()
OccurenceQuery	getOccurenceQuery()
Person	getPerson(java.lang.String titleCache)
java.util.Map<java.lang.String,Person>	getPersons()
OccurenceQuery	getQuery()
java.net.URI	getReportUri()
java.lang.String	getSourceReferenceTitle()
SpecimenUserInteraction	getSpecimenUserInteraction()
java.lang.String	getTaxonReference()
java.util.Map<java.util.UUID,java.util.UUID>	getTaxonToDescriptionMap()
Team	getTeam(java.lang.String titleCache)
java.util.Map<java.lang.String,Team>	getTeams()
java.util.Map<java.lang.String,Person>	getTitleCachePerson()
java.util.Map<java.lang.String,Team>	getTitleCacheTeam()
SpecimenOrObservationType	getType()
boolean	isAddIndividualsAssociationsSuchAsSpecimenAndObservations()
boolean	isAddMediaAsMediaSpecimen()
boolean	isAllowReuseOtherClassifications()
boolean	isDeduplicateClassifications()
boolean	isDeduplicateReferences()
boolean	isDownloadSequenceData()
boolean	isIgnoreAuthorship()
boolean	isIgnoreImportOfExistingSpecimen()
boolean	isMapUnitIdToAccessionNumber()
boolean	isMapUnitIdToBarcode()
boolean	isMapUnitIdToCatalogNumber()
boolean	isMoveNewTaxaToDefaultClassification()
boolean	isOverwriteExistingSpecimens()
boolean	isRemoveCountryFromLocalityText()
boolean	isReuseExistingDescriptiveGroups()
boolean	isReuseExistingMetaData()
boolean	isReuseExistingTaxaWhenPossible()
boolean	isValid()
void	putNamedAreaDecision(java.lang.String areaStr, java.util.UUID uuid)
void	setAddIndividualsAssociationsSuchAsSpecimenAndObservations(boolean addIndividualsAssociationsSuchAsSpecimenAndObservations)
void	setAddMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen)
void	setAllowReuseOtherClassifications(boolean allowReuseOtherClassifications)
void	setDeduplicateClassifications(boolean deduplicateClassifications)
void	setDeduplicateReferences(boolean deduplicateReferences)
void	setDefaultAuthor(java.lang.String defaultAuthor)
void	setDownloadSequenceData(boolean downloadSequenceData)
void	setIgnoreAuthorship(boolean ignoreAuthorship)
void	setIgnoreImportOfExistingSpecimen(boolean ignoreImportOfExistingSpecimen)
void	setMapUnitIdToAccessionNumber(boolean mapUnitIdToAccessionNumber)
void	setMapUnitIdToBarcode(boolean mapUnitIdToBarcode)
void	setMapUnitIdToCatalogNumber(boolean mapUnitIdToCatalogNumber)
void	setMoveNewTaxaToDefaultClassification(boolean moveNewTaxaToDefaultClassification)
void	setNamedAreaDecisions(java.util.Map<java.lang.String,java.util.UUID> namedAreaDecisions)
void	setOccurenceQuery(OccurenceQuery query)
void	setOverwriteExistingSpecimens(boolean overwriteExistingSpecimens)
void	setPersons(java.util.Map<java.lang.String,Person> titleCachePerson)
void	setQuery(OccurenceQuery query)
void	setRemoveCountryFromLocalityText(boolean removeCountryFromLocalityText)
void	setReportUri(java.net.URI reportUri)
void	setReuseExistingDescriptiveGroups(boolean reuseExistingDescriptiveGroups)
void	setReuseExistingMetaData(boolean reuseExistingMetaData)
void	setReuseExistingTaxaWhenPossible(boolean reuseExistingTaxaWhenPossible)
void	setSourceReferenceTitle(java.lang.String name)
void	setTaxonReference(java.lang.String taxonReference)
void	setTeams(java.util.Map<java.lang.String,Team> titleCacheTeam)
void	setTitleCachePerson(java.util.Map<java.lang.String,Person> titleCachePerson)
void	setTitleCacheTeam(java.util.Map<java.lang.String,Team> titleCacheTeam)
void	setType(SpecimenOrObservationType type)

Methods inherited from class eu.etaxonomy.cdm.io.common.ImportConfiguratorBase

getAuthenticationToken, getCheck, getClassificationName, getClassificationUuid, getCommentator, getDateString, getDefaultFunction, getDestination, getDestinationNameString, getEditor, getFeatureMap, getFeatureTreeTitle, getIoClassList, getNomenclaturalCode, getSecUuid, getSource, getSourceNameString, getSourceReference, getSourceRefUuid, getSourceSecId, getTransformer, getUuidFeatureTree, isCreateNew, isInteractWithUser, isOmitTermLoading, isRegisterAuditing, makeIoClassList, setCheck, setClassificationName, setClassificationUuid, setCommentator, setDestination, setEditor, setFeatureMap, setFeatureTreeTitle, setInteractWithUser, setIoClassList, setIoClassList, setNomenclaturalCode, setRegisterAuditing, setSecUuid, setSource, setSourceReference, setSourceRefUuid, setSourceSecId, setTransformer, setUuidFeatureTree

Methods inherited from class eu.etaxonomy.cdm.io.common.IoConfiguratorBase

authenticateAsDefaultAdmin, getCdmAppController, getDbSchemaValidation, getHibernateConfig, getProgressMonitor, getUserFriendlyIOName, isUseClassification, setAuthentication, setAuthenticationToken, setCdmAppController, setDbSchemaValidation, setProgressMonitor, setUseClassification, setUserFriendlyIOName

Methods inherited from class eu.etaxonomy.cdm.io.common.ObservableBase

addObserver, addObservers, countObservers, fire, fireWarningEvent, fireWarningEvent, getObservers, removeObserver, removeObservers, setObservers

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface eu.etaxonomy.cdm.io.common.IImportConfigurator

getDbSchemaValidation, getNewState, setDbSchemaValidation

Methods inherited from interface eu.etaxonomy.cdm.io.common.IIoConfigurator

authenticateAsDefaultAdmin, getCdmAppController, getHibernateConfig, getObservers, getProgressMonitor, getUserFriendlyIOName, setAuthentication, setAuthenticationToken, setCdmAppController, setObservers, setProgressMonitor

Methods inherited from interface eu.etaxonomy.cdm.io.common.IIoObservable

addObserver, addObservers, countObservers, removeObserver, removeObservers

Field Detail

query

protected OccurenceQuery query

namedAreaDecisions

protected java.util.Map<java.lang.String,java.util.UUID> namedAreaDecisions

Constructor Detail

SpecimenImportConfiguratorBase

public SpecimenImportConfiguratorBase(IInputTransformer transformer)

Parameters:

transformer -

Method Detail

getType

public SpecimenOrObservationType getType()

Returns:

the type

setType

public void setType(SpecimenOrObservationType type)

Parameters:

type - the type to set

isIgnoreImportOfExistingSpecimen

public boolean isIgnoreImportOfExistingSpecimen()

setIgnoreImportOfExistingSpecimen

public void setIgnoreImportOfExistingSpecimen(boolean ignoreImportOfExistingSpecimen)

getTitleCacheTeam

public java.util.Map<java.lang.String,Team> getTitleCacheTeam()

setTitleCacheTeam

public void setTitleCacheTeam(java.util.Map<java.lang.String,Team> titleCacheTeam)

getTitleCachePerson

public java.util.Map<java.lang.String,Person> getTitleCachePerson()

setTitleCachePerson

public void setTitleCachePerson(java.util.Map<java.lang.String,Person> titleCachePerson)

getQuery

public OccurenceQuery getQuery()

setQuery

public void setQuery(OccurenceQuery query)

getTaxonReference

public java.lang.String getTaxonReference()

setTaxonReference

public void setTaxonReference(java.lang.String taxonReference)

isAddIndividualsAssociationsSuchAsSpecimenAndObservations

public boolean isAddIndividualsAssociationsSuchAsSpecimenAndObservations()

setAddIndividualsAssociationsSuchAsSpecimenAndObservations

public void setAddIndividualsAssociationsSuchAsSpecimenAndObservations(boolean addIndividualsAssociationsSuchAsSpecimenAndObservations)

isReuseExistingDescriptiveGroups

public boolean isReuseExistingDescriptiveGroups()

setReuseExistingDescriptiveGroups

public void setReuseExistingDescriptiveGroups(boolean reuseExistingDescriptiveGroups)

getDefaultAuthor

public java.lang.String getDefaultAuthor()

setDefaultAuthor

public void setDefaultAuthor(java.lang.String defaultAuthor)

isAllowReuseOtherClassifications

public boolean isAllowReuseOtherClassifications()

setAllowReuseOtherClassifications

public void setAllowReuseOtherClassifications(boolean allowReuseOtherClassifications)

isDeduplicateReferences

public boolean isDeduplicateReferences()

setDeduplicateReferences

public void setDeduplicateReferences(boolean deduplicateReferences)

isDeduplicateClassifications

public boolean isDeduplicateClassifications()

setDeduplicateClassifications

public void setDeduplicateClassifications(boolean deduplicateClassifications)

isMoveNewTaxaToDefaultClassification

public boolean isMoveNewTaxaToDefaultClassification()

setMoveNewTaxaToDefaultClassification

public void setMoveNewTaxaToDefaultClassification(boolean moveNewTaxaToDefaultClassification)

isMapUnitIdToCatalogNumber

public boolean isMapUnitIdToCatalogNumber()

setMapUnitIdToCatalogNumber

public void setMapUnitIdToCatalogNumber(boolean mapUnitIdToCatalogNumber)

isMapUnitIdToAccessionNumber

public boolean isMapUnitIdToAccessionNumber()

setMapUnitIdToAccessionNumber

public void setMapUnitIdToAccessionNumber(boolean mapUnitIdToAccessionNumber)

isMapUnitIdToBarcode

public boolean isMapUnitIdToBarcode()

setMapUnitIdToBarcode

public void setMapUnitIdToBarcode(boolean mapUnitIdToBarcode)

getNamedAreaDecisions

public java.util.Map<java.lang.String,java.util.UUID> getNamedAreaDecisions()

setNamedAreaDecisions

public void setNamedAreaDecisions(java.util.Map<java.lang.String,java.util.UUID> namedAreaDecisions)

putNamedAreaDecision

public void putNamedAreaDecision(java.lang.String areaStr,
                                 java.util.UUID uuid)

getNamedAreaDecision

public java.util.UUID getNamedAreaDecision(java.lang.String areaStr)

getTaxonToDescriptionMap

public java.util.Map<java.util.UUID,java.util.UUID> getTaxonToDescriptionMap()

getSpecimenUserInteraction

public SpecimenUserInteraction getSpecimenUserInteraction()

setReuseExistingTaxaWhenPossible

public void setReuseExistingTaxaWhenPossible(boolean reuseExistingTaxaWhenPossible)

setIgnoreAuthorship

public void setIgnoreAuthorship(boolean ignoreAuthorship)

setRemoveCountryFromLocalityText

public void setRemoveCountryFromLocalityText(boolean removeCountryFromLocalityText)

setAddMediaAsMediaSpecimen

public void setAddMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen)

setOverwriteExistingSpecimens

public void setOverwriteExistingSpecimens(boolean overwriteExistingSpecimens)

isOverwriteExistingSpecimens

public boolean isOverwriteExistingSpecimens()

isReuseExistingTaxaWhenPossible

public boolean isReuseExistingTaxaWhenPossible()

Returns:

setTeams

public void setTeams(java.util.Map<java.lang.String,Team> titleCacheTeam)

Parameters:

titleCacheTeam -

getTeam

public Team getTeam(java.lang.String titleCache)

getTeams

public java.util.Map<java.lang.String,Team> getTeams()

setPersons

public void setPersons(java.util.Map<java.lang.String,Person> titleCachePerson)

Parameters:

titleCachePerson -

getPersons

public java.util.Map<java.lang.String,Person> getPersons()

getPerson

public Person getPerson(java.lang.String titleCache)

isAddMediaAsMediaSpecimen

public boolean isAddMediaAsMediaSpecimen()

addMediaAsMediaSpecimen

public void addMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen)

isIgnoreAuthorship

public boolean isIgnoreAuthorship()

Returns:

isRemoveCountryFromLocalityText

public boolean isRemoveCountryFromLocalityText()

Returns:

getOccurenceQuery

public OccurenceQuery getOccurenceQuery()

setOccurenceQuery

public void setOccurenceQuery(OccurenceQuery query)

isReuseExistingMetaData

public boolean isReuseExistingMetaData()

Returns:

the reuseExistingMetaData

setReuseExistingMetaData

public void setReuseExistingMetaData(boolean reuseExistingMetaData)

Parameters:

reuseExistingMetaData - the reuseExistingMetaData to set

setReportUri

public void setReportUri(java.net.URI reportUri)

getReportUri

public java.net.URI getReportUri()

getSourceReferenceTitle

public java.lang.String getSourceReferenceTitle()

Specified by:

getSourceReferenceTitle in interface IImportConfigurator

Overrides:

getSourceReferenceTitle in class ImportConfiguratorBase<STATE extends SpecimenImportStateBase<CONFIG,STATE>,InputStream>

setSourceReferenceTitle

public void setSourceReferenceTitle(java.lang.String name)

Specified by:

setSourceReferenceTitle in interface IImportConfigurator

Overrides:

setSourceReferenceTitle in class ImportConfiguratorBase<STATE extends SpecimenImportStateBase<CONFIG,STATE>,InputStream>

isValid

public boolean isValid()

Specified by:

isValid in interface IImportConfigurator

Overrides:

isValid in class ImportConfiguratorBase<STATE extends SpecimenImportStateBase<CONFIG,STATE>,InputStream>

isDownloadSequenceData

public boolean isDownloadSequenceData()

setDownloadSequenceData

public void setDownloadSequenceData(boolean downloadSequenceData)