-// $Id$\r
-/**\r
-* Copyright (C) 2016 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.cdm.io.specimen;\r
-\r
-import java.util.Map;\r
-\r
-import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;\r
-import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;\r
-import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;\r
-import eu.etaxonomy.cdm.model.agent.Person;\r
-import eu.etaxonomy.cdm.model.agent.Team;\r
-\r
-/**\r
- * @author k.luther\r
- * @date 15.07.2016\r
- *\r
- */\r
-public abstract class SpecimenImportConfiguratorBase<STATE extends SpecimenImportStateBase, InputStream> extends ImportConfiguratorBase<STATE, InputStream> {\r
-\r
- private boolean ignoreImportOfExistingSpecimen;\r
- private boolean reuseExistingTaxaWhenPossible;\r
- private Map<String, Team> teams;\r
- private Map<String, Person> persons;\r
- private boolean ignoreAuthorship;\r
- private boolean removeCountryFromLocalityText;\r
- private OccurenceQuery query ;\r
-\r
- /**\r
- * @param transformer\r
- */\r
- public SpecimenImportConfiguratorBase(IInputTransformer transformer) {\r
- super(transformer);\r
- // TODO Auto-generated constructor stub\r
- }\r
-\r
- /**\r
- * @return\r
- */\r
- public boolean isReuseExistingTaxaWhenPossible() {\r
-\r
- return reuseExistingTaxaWhenPossible;\r
- }\r
-\r
- /**\r
- * @param titleCacheTeam\r
- */\r
- public void setTeams(Map<String, Team> titleCacheTeam) {\r
- this.teams = titleCacheTeam;\r
-\r
- }\r
-\r
- /**\r
- * @param titleCachePerson\r
- */\r
- public void setPersons(Map<String, Person> titleCachePerson) {\r
- this.persons = titleCachePerson;\r
- }\r
-\r
- /**\r
- * @return\r
- */\r
- public boolean isIgnoreAuthorship() {\r
- return ignoreAuthorship;\r
- }\r
-\r
- /**\r
- * @return\r
- */\r
- public boolean isRemoveCountryFromLocalityText() {\r
- return removeCountryFromLocalityText;\r
- }\r
-\r
- public boolean isIgnoreImportOfExistingSpecimens(){\r
- return ignoreImportOfExistingSpecimen;\r
- }\r
-\r
- public OccurenceQuery getOccurenceQuery(){\r
- return query;\r
- }\r
-\r
- public void setOccurenceQuery(OccurenceQuery query){\r
- this.query = query;\r
- }\r
-\r
-}\r
+/**
+* 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 java.net.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;
+ }
+
+
+
+}
BGBM BDI Projects / cdmlib.git / blobdiff