EDIT

/**

* Copyright (C) 2016 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.specimen;

import eu.etaxonomy.cdm.common.URI;

import java.util.HashMap;

import java.util.Map;

import java.util.UUID;

import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;

import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;

import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;

import eu.etaxonomy.cdm.model.agent.Person;

import eu.etaxonomy.cdm.model.agent.Team;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;

/**

 * @author k.luther

 * @since 15.07.2016

 *

 */

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

        extends ImportConfiguratorBase<STATE, InputStream> {

    private static final long serialVersionUID = 4741134251527063988L;

    /**

     * @param transformer

     */

    public SpecimenImportConfiguratorBase(IInputTransformer transformer) {

        super(transformer);

    }

    private boolean ignoreImportOfExistingSpecimen = true;

    private boolean reuseExistingTaxaWhenPossible = true;

    private final Map<UUID, UUID> taxonToDescriptionMap = new HashMap<UUID, UUID>();

    private Map<String, Team> titleCacheTeam;

    private Map<String, Person> titleCachePerson;

    private boolean ignoreAuthorship = false;

    private boolean removeCountryFromLocalityText = false;

    protected OccurenceQuery query ;

    private boolean addMediaAsMediaSpecimen = false;

    private boolean reuseExistingMetaData = true;

    private String sourceReferenceTitle = null;

    private String taxonReference = null;

    private boolean addIndividualsAssociationsSuchAsSpecimenAndObservations = true;

    private boolean reuseExistingDescriptiveGroups = false;

    private String defaultAuthor="";

    private boolean allowReuseOtherClassifications =true;

    private boolean deduplicateReferences = false;

    private boolean deduplicateClassifications = false;

    private boolean moveNewTaxaToDefaultClassification = true;

    private boolean mapUnitIdToCatalogNumber = true;

    private boolean mapUnitIdToAccessionNumber = false;

    private boolean mapUnitIdToBarcode = false;

    private boolean overwriteExistingSpecimens = false;

    private boolean downloadSequenceData = false;

    private SpecimenOrObservationType type;

    /**

     * @return the type

     */

    public SpecimenOrObservationType getType() {

        return type;

    }

    /**

     * @param type the type to set

     */

    public void setType(SpecimenOrObservationType type) {

        this.type = type;

    }

    private final SpecimenUserInteraction specimenUserInteraction = new SpecimenUserInteraction();

    protected Map<String,UUID> namedAreaDecisions = new HashMap<String,UUID>();

    private URI reportUri;

    public boolean isIgnoreImportOfExistingSpecimen() {

        return ignoreImportOfExistingSpecimen;

    }

    public void setIgnoreImportOfExistingSpecimen(boolean ignoreImportOfExistingSpecimen) {

        this.ignoreImportOfExistingSpecimen = ignoreImportOfExistingSpecimen;

    }

    public Map<String, Team> getTitleCacheTeam() {

        return titleCacheTeam;

    }

    public void setTitleCacheTeam(Map<String, Team> titleCacheTeam) {

        this.titleCacheTeam = titleCacheTeam;

    }

    public Map<String, Person> getTitleCachePerson() {

        return titleCachePerson;

    }

    public void setTitleCachePerson(Map<String, Person> titleCachePerson) {

        this.titleCachePerson = titleCachePerson;

    }

    public OccurenceQuery getQuery() {

        return query;

    }

    public void setQuery(OccurenceQuery query) {

        this.query = query;

    }

    public String getTaxonReference() {

        return taxonReference;

    }

    public void setTaxonReference(String taxonReference) {

        this.taxonReference = taxonReference;

    }

    public boolean isAddIndividualsAssociationsSuchAsSpecimenAndObservations() {

        return addIndividualsAssociationsSuchAsSpecimenAndObservations;

    }

    public void setAddIndividualsAssociationsSuchAsSpecimenAndObservations(

            boolean addIndividualsAssociationsSuchAsSpecimenAndObservations) {

        this.addIndividualsAssociationsSuchAsSpecimenAndObservations = addIndividualsAssociationsSuchAsSpecimenAndObservations;

    }

    public boolean isReuseExistingDescriptiveGroups() {

        return reuseExistingDescriptiveGroups;

    }

    public void setReuseExistingDescriptiveGroups(boolean reuseExistingDescriptiveGroups) {

        this.reuseExistingDescriptiveGroups = reuseExistingDescriptiveGroups;

    }

    public String getDefaultAuthor() {

        return defaultAuthor;

    }

    public void setDefaultAuthor(String defaultAuthor) {

        this.defaultAuthor = defaultAuthor;

    }

    public boolean isAllowReuseOtherClassifications() {

        return allowReuseOtherClassifications;

    }

    public void setAllowReuseOtherClassifications(boolean allowReuseOtherClassifications) {

        this.allowReuseOtherClassifications = allowReuseOtherClassifications;

    }

    public boolean isDeduplicateReferences() {

        return deduplicateReferences;

    }

    public void setDeduplicateReferences(boolean deduplicateReferences) {

        this.deduplicateReferences = deduplicateReferences;

    }

    public boolean isDeduplicateClassifications() {

        return deduplicateClassifications;

    }

    public void setDeduplicateClassifications(boolean deduplicateClassifications) {

        this.deduplicateClassifications = deduplicateClassifications;

    }

    public boolean isMoveNewTaxaToDefaultClassification() {

        return moveNewTaxaToDefaultClassification;

    }

    public void setMoveNewTaxaToDefaultClassification(boolean moveNewTaxaToDefaultClassification) {

        this.moveNewTaxaToDefaultClassification = moveNewTaxaToDefaultClassification;

    }

    public boolean isMapUnitIdToCatalogNumber() {

        return mapUnitIdToCatalogNumber;

    }

    public void setMapUnitIdToCatalogNumber(boolean mapUnitIdToCatalogNumber) {

        this.mapUnitIdToCatalogNumber = mapUnitIdToCatalogNumber;

    }

    public boolean isMapUnitIdToAccessionNumber() {

        return mapUnitIdToAccessionNumber;

    }

    public void setMapUnitIdToAccessionNumber(boolean mapUnitIdToAccessionNumber) {

        this.mapUnitIdToAccessionNumber = mapUnitIdToAccessionNumber;

    }

    public boolean isMapUnitIdToBarcode() {

        return mapUnitIdToBarcode;

    }

    public void setMapUnitIdToBarcode(boolean mapUnitIdToBarcode) {

        this.mapUnitIdToBarcode = mapUnitIdToBarcode;

    }

    public Map<String, UUID> getNamedAreaDecisions() {

        return namedAreaDecisions;

    }

    public void setNamedAreaDecisions(Map<String,UUID> namedAreaDecisions) {

        this.namedAreaDecisions = namedAreaDecisions;

    }

    public void putNamedAreaDecision(String areaStr,UUID uuid){

        this.namedAreaDecisions.put(areaStr,uuid);

    }

    public UUID getNamedAreaDecision(String areaStr){

        return namedAreaDecisions.get(areaStr);

    }

    public Map<UUID, UUID> getTaxonToDescriptionMap() {

        return taxonToDescriptionMap;

    }

    public SpecimenUserInteraction getSpecimenUserInteraction() {

        return specimenUserInteraction;

    }

    public void setReuseExistingTaxaWhenPossible(boolean reuseExistingTaxaWhenPossible) {

        this.reuseExistingTaxaWhenPossible = reuseExistingTaxaWhenPossible;

    }

    public void setIgnoreAuthorship(boolean ignoreAuthorship) {

        this.ignoreAuthorship = ignoreAuthorship;

    }

    public void setRemoveCountryFromLocalityText(boolean removeCountryFromLocalityText) {

        this.removeCountryFromLocalityText = removeCountryFromLocalityText;

    }

    public void setAddMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen) {

        this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;

    }

    public void setOverwriteExistingSpecimens(boolean overwriteExistingSpecimens) {

        this.overwriteExistingSpecimens = overwriteExistingSpecimens;

    }

    public boolean isOverwriteExistingSpecimens(){

        return overwriteExistingSpecimens;

    }

    /**

     * @return

     */

    public boolean isReuseExistingTaxaWhenPossible() {

        return reuseExistingTaxaWhenPossible;

    }

    /**

     * @param titleCacheTeam

     */

    public void setTeams(Map<String, Team> titleCacheTeam) {

       this.titleCacheTeam  = titleCacheTeam;

    }

    public Team getTeam(String titleCache){

        return titleCacheTeam.get(titleCache);

    }

    public Map<String, Team> getTeams(){

        return titleCacheTeam;

    }

    /**

     * @param titleCachePerson

     */

    public void setPersons(Map<String, Person> titleCachePerson) {

        this.titleCachePerson = titleCachePerson;

    }

    public Map<String, Person> getPersons(){

        return titleCachePerson;

    }

    public Person getPerson(String titleCache){

        return titleCachePerson.get(titleCache);

    }

    public boolean isAddMediaAsMediaSpecimen(){

        return addMediaAsMediaSpecimen;

    }

    public void addMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen){

       this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;

    }

    /**

     * @return

     */

    public boolean isIgnoreAuthorship() {

        return ignoreAuthorship;

    }

    /**

     * @return

     */

    public boolean isRemoveCountryFromLocalityText() {

        return removeCountryFromLocalityText;

    }

    public OccurenceQuery getOccurenceQuery(){

        return query;

    }

    public void setOccurenceQuery(OccurenceQuery query){

        this.query = query;

    }

    /**

     * @return the reuseExistingMetaData

     */

    public boolean isReuseExistingMetaData() {

        return reuseExistingMetaData;

    }

    /**

     * @param reuseExistingMetaData the reuseExistingMetaData to set

     */

    public void setReuseExistingMetaData(boolean reuseExistingMetaData) {

        this.reuseExistingMetaData = reuseExistingMetaData;

    }

    public void setReportUri(URI reportUri) {

        this.reportUri = reportUri;

    }

    public URI getReportUri() {

        return reportUri;

    }

    @Override

    public String getSourceReferenceTitle(){

        return this.sourceReferenceTitle;

    }

    @Override

    public void setSourceReferenceTitle(String name){

        this.sourceReferenceTitle=name;

    }

    @Override

    public boolean isValid(){

        return true;

    }

    public boolean isDownloadSequenceData() {

        return downloadSequenceData;

    }

    public void setDownloadSequenceData(boolean downloadSequenceData) {

        this.downloadSequenceData = downloadSequenceData;

    }

}