/**
* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
+* 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.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.UUID;
+
import org.apache.log4j.Logger;
+import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
+import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
+import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;
+import eu.etaxonomy.cdm.api.service.pager.Pager;
+import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.io.common.CdmImportBase;
import eu.etaxonomy.cdm.io.common.IImportConfigurator;
-import eu.etaxonomy.cdm.io.common.ImportStateBase;
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.Identification;
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;
+import eu.etaxonomy.cdm.model.agent.AgentBase;
+import eu.etaxonomy.cdm.model.agent.Institution;
+import eu.etaxonomy.cdm.model.agent.Team;
+import eu.etaxonomy.cdm.model.common.CdmBase;
+import eu.etaxonomy.cdm.model.common.ISourceable;
+import eu.etaxonomy.cdm.model.common.IdentifiableSource;
+import eu.etaxonomy.cdm.model.common.LanguageString;
+import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
+import eu.etaxonomy.cdm.model.common.OriginalSourceType;
+import eu.etaxonomy.cdm.model.description.DescriptionBase;
+import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
+import eu.etaxonomy.cdm.model.description.Feature;
+import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
+import eu.etaxonomy.cdm.model.description.TaxonDescription;
+import eu.etaxonomy.cdm.model.name.BacterialName;
+import eu.etaxonomy.cdm.model.name.BotanicalName;
+import eu.etaxonomy.cdm.model.name.CultivarPlantName;
+import eu.etaxonomy.cdm.model.name.INonViralName;
+import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
+import eu.etaxonomy.cdm.model.name.NonViralName;
+import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
+import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;
+import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
+import eu.etaxonomy.cdm.model.occurrence.Collection;
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
+import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
+import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
+import eu.etaxonomy.cdm.model.taxon.Classification;
+import eu.etaxonomy.cdm.model.taxon.Synonym;
+import eu.etaxonomy.cdm.model.taxon.Taxon;
+import eu.etaxonomy.cdm.model.taxon.TaxonBase;
+import eu.etaxonomy.cdm.model.taxon.TaxonNode;
+import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
+import eu.etaxonomy.cdm.persistence.query.MatchMode;
+import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
+import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
/**
* @author p.kelbert
* @created 20.10.2008
*/
-public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STATE extends ImportStateBase> extends CdmImportBase<CONFIG, STATE> {
- @SuppressWarnings("unused")
- private static final Logger logger = Logger.getLogger(SpecimenImportBase.class);
+public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STATE extends SpecimenImportStateBase> extends CdmImportBase<CONFIG, STATE> {
+
+ private static final long serialVersionUID = 4423065367998125678L;
+ private static final Logger logger = Logger.getLogger(SpecimenImportBase.class);
+ protected final boolean DEBUG = true;
+
+ protected static final UUID SPECIMEN_SCAN_TERM = UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03");
+
+ private static final String COLON = ":";
+
+
+ @Override
+ protected abstract void doInvoke(STATE state);
+
+ /**
+ * Handle a single unit
+ * @param state
+ * @param item
+ */
+ protected abstract void handleSingleUnit(STATE state, Object item) ;
+
+
+
+ protected TaxonNameBase<?, ?> getOrCreateTaxonName(String scientificName, Rank rank, boolean preferredFlag, STATE state, int unitIndexInAbcdFile){
+ TaxonNameBase<?, ?> taxonName = null;
+ SpecimenImportConfiguratorBase<?,?> config = state.getConfig();
+
+ //check atomised name data for rank
+ //new name will be created
+ TaxonNameBase<?,?> atomisedTaxonName = null;
+ if (rank==null && unitIndexInAbcdFile>=0 && ((state.getDataHolder().getAtomisedIdentificationList() != null && !state.getDataHolder().getAtomisedIdentificationList().isEmpty())|| state.getDataHolder().getAtomisedIdentificationList().size() > 0)) {
+ atomisedTaxonName = setTaxonNameByType(state.getDataHolder().getAtomisedIdentificationList().get(unitIndexInAbcdFile), scientificName, state);
+ if(atomisedTaxonName!=null){
+ rank = atomisedTaxonName.getRank();
+ }
+ }
+ if(config.isReuseExistingTaxaWhenPossible()){
+ TaxonNameBase<?,?> parsedName = atomisedTaxonName;
+ if(parsedName==null){
+ parsedName = parseScientificName(scientificName, state, state.getReport());
+ }
+ atomisedTaxonName = parsedName;
+ if(config.isIgnoreAuthorship() && parsedName!=null && preferredFlag){
+ // do not ignore authorship for non-preferred names because they need
+ // to be created for the determination history
+ String nameCache = parsedName.getNameCache();
+ List<NonViralName> names = getNameService().findNamesByNameCache(nameCache, MatchMode.EXACT, null);
+ if (!names.isEmpty()){
+ return getBestMatchingName(scientificName, new ArrayList<TaxonNameBase>(names), state);
+ }
+ } else {
+ //search for existing names
+ List<TaxonNameBase> names = getNameService().listByTitle(TaxonNameBase.class, scientificName, MatchMode.EXACT, null, null, null, null, null);
+ taxonName = getBestMatchingName(scientificName, names, state);
+ //still nothing found -> try with the atomised name full title cache
+ if(taxonName==null && atomisedTaxonName!=null){
+ names = getNameService().listByTitle(TaxonNameBase.class, atomisedTaxonName.getFullTitleCache(), MatchMode.EXACT, null, null, null, null, null);
+ taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state);
+ //still nothing found -> try with the atomised name title cache
+ if(taxonName==null){
+ names = getNameService().listByTitle(TaxonNameBase.class, atomisedTaxonName.getTitleCache(), MatchMode.EXACT, null, null, null, null, null);
+ taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state);
+ }
+ }
+
+ }
+
+ }
+
+ if(taxonName==null && atomisedTaxonName!=null){
+ taxonName = atomisedTaxonName;
+ state.getReport().addName(taxonName);
+ logger.info("Created new taxon name "+taxonName);
+ if(taxonName.hasProblem()){
+ state.getReport().addInfoMessage(String.format("Created %s with parsing problems", taxonName));
+ }
+ if(!atomisedTaxonName.getTitleCache().equals(scientificName)){
+ state.getReport().addInfoMessage(String.format("Taxon %s was parsed as %s", scientificName, atomisedTaxonName.getTitleCache()));
+ }
+ }
+ else if(taxonName==null){
+ //create new taxon name
+
+ if (state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP)){
+ taxonName = TaxonNameBase.NewBotanicalInstance(rank);
+ }else if (state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICZN)){
+ taxonName = TaxonNameBase.NewZoologicalInstance(rank);
+ }else{
+ taxonName = TaxonNameFactory.NewNonViralInstance(rank);
+ }
+ taxonName.setFullTitleCache(scientificName,true);
+ taxonName.setTitleCache(scientificName, true);
+ state.getReport().addName(taxonName);
+ logger.info("Created new taxon name "+taxonName);
+ }
+ save(taxonName, state);
+ return taxonName;
+ }
+
+ protected TaxonNameBase<?, ?> getBestMatchingName(String scientificName, java.util.Collection<TaxonNameBase> names, STATE state){
+ List<TaxonNameBase> namesWithAcceptedTaxa = new ArrayList<>();
+ for (TaxonNameBase name : names) {
+ if(!name.getTaxa().isEmpty()){
+ namesWithAcceptedTaxa.add(name);
+ }
+ }
+ String message = "More than one taxon name was found for "+scientificName+"!";
+ //check for names with accepted taxa
+ if(namesWithAcceptedTaxa.size()>0){
+ if(namesWithAcceptedTaxa.size()>1){
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ return null;
+ }
+ return namesWithAcceptedTaxa.iterator().next();
+ }
+ //no names with accepted taxa found -> check accepted taxa of synonyms
+ List<Taxon> taxaFromSynonyms = new ArrayList<>();
+ for (TaxonNameBase name : names) {
+ Set<TaxonBase> taxonBases = name.getTaxonBases();
+ for (TaxonBase taxonBase : taxonBases) {
+ if(taxonBase.isInstanceOf(Synonym.class)){
+ Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
+ taxaFromSynonyms.add(synonym.getAcceptedTaxon());
+ }
+ }
+ }
+ if(taxaFromSynonyms.size()>0){
+ if(taxaFromSynonyms.size()>1){
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ return null;
+ }
+ return taxaFromSynonyms.iterator().next().getName();
+ }
+ return null;
+ }
+ /**
+ * Parse automatically the scientific name
+ * @param scientificName the scientific name to parse
+ * @param state the current import state
+ * @param report the import report
+ * @return a parsed name
+ */
+ protected TaxonNameBase<?,?> parseScientificName(String scientificName, STATE state, SpecimenImportReport report) {
+ NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
+ TaxonNameBase<?,?> taxonName = null;
+ boolean problem = false;
+
+ if(DEBUG){
+ logger.info("parseScientificName " + state.getDataHolder().getNomenclatureCode().toString());
+ }
+
+ if (state.getDataHolder().getNomenclatureCode().toString().equals("Zoological") || state.getDataHolder().getNomenclatureCode().toString().contains("ICZN")) {
+ taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, null);
+ if (taxonName.hasProblem()) {
+ problem = true;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().toString().equals("Botanical") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
+ taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, null);
+ if (taxonName.hasProblem()) {
+ problem = true;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().toString().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
+ taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNB, null);
+ if (taxonName.hasProblem()) {
+ problem = true;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().toString().equals("Cultivar") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNCP")) {
+ taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, null);
+ if (taxonName.hasProblem()) {
+ problem = true;
+ }
+ }
+ if (problem) {
+ String message = String.format("Parsing problems for %s", scientificName);
+ if(taxonName!=null){
+ for (ParserProblem parserProblem : taxonName.getParsingProblems()) {
+ message += "\n\t- "+parserProblem;
+ }
+ }
+ report.addInfoMessage(message);
+ logger.info(message);
+ }
+ return taxonName;
+
+ }
+
+ /**
+ * Create the name without automatic parsing, either because it failed, or because the user deactivated it.
+ * The name is built upon the ABCD fields
+ * @param atomisedMap : the ABCD atomised fields
+ * @param fullName : the full scientific name
+ * @param state
+ * @return the corresponding Botanical or Zoological or... name
+ */
+ protected TaxonNameBase<?,?> setTaxonNameByType(
+ HashMap<String, String> atomisedMap, String fullName, STATE state) {
+ boolean problem = false;
+ if(DEBUG) {
+ logger.info("settaxonnamebytype " + state.getDataHolder().getNomenclatureCode().toString());
+ }
+
+ if (state.getDataHolder().getNomenclatureCode().equals("Zoological") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICZN.getUuid())) {
+ TaxonNameBase<?,?> taxonName = TaxonNameBase.NewZoologicalInstance(null);
+ taxonName.setFullTitleCache(fullName, true);
+ taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
+ taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
+ taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap,"SpeciesEpithet")));
+ taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap,"SubspeciesEpithet")));
+
+ if (taxonName.getGenusOrUninomial() != null){
+ taxonName.setRank(Rank.GENUS());
+ }
+
+ if (taxonName.getInfraGenericEpithet() != null){
+ taxonName.setRank(Rank.SUBGENUS());
+ }
+
+ if (taxonName.getSpecificEpithet() != null){
+ taxonName.setRank(Rank.SPECIES());
+ }
+
+ if (taxonName.getInfraSpecificEpithet() != null){
+ taxonName.setRank(Rank.SUBSPECIES());
+ }
+
+ Team team = null;
+ if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
+ }
+ else {
+ if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
+ }
+ }
+ if (team != null) {
+ taxonName.setBasionymAuthorship(team);
+ }
+ else {
+ if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
+ taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
+ }
+ else if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
+ taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamAndYear"));
+ }
+ }
+ if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
+ taxonName.setCombinationAuthorship(team);
+ }
+ if (taxonName.hasProblem()) {
+ logger.info("pb ICZN");
+ problem = true;
+ }
+ else {
+ return taxonName;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().equals("Botanical") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP.getUuid())) {
+ BotanicalName taxonName = (BotanicalName) parseScientificName(fullName, state, state.getReport());
+ if (taxonName != null){
+ return taxonName;
+ }
+ else{
+ taxonName = TaxonNameBase.NewBotanicalInstance(null);
+ }
+ taxonName.setFullTitleCache(fullName, true);
+ taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
+ taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "FirstEpithet")));
+ taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "InfraSpeEpithet")));
+ try {
+ taxonName.setRank(Rank.getRankByName(getFromMap(atomisedMap, "Rank")));
+ } catch (Exception e) {
+ if (taxonName.getInfraSpecificEpithet() != null){
+ taxonName.setRank(Rank.SUBSPECIES());
+ }
+ else if (taxonName.getSpecificEpithet() != null){
+ taxonName.setRank(Rank.SPECIES());
+ }
+ else if (taxonName.getInfraGenericEpithet() != null){
+ taxonName.setRank(Rank.SUBGENUS());
+ }
+ else if (taxonName.getGenusOrUninomial() != null){
+ taxonName.setRank(Rank.GENUS());
+ }
+ }
+ Team team = null;
+ if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
+ taxonName.setBasionymAuthorship(team);
+ }
+ if (getFromMap(atomisedMap, "AuthorTeam") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeam"), true);
+ taxonName.setCombinationAuthorship(team);
+ }
+ if (team == null) {
+ if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
+ taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
+ }
+ else if (getFromMap(atomisedMap, "AuthorTeam") != null) {
+ taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeam"));
+ }
+ }
+ if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
+ taxonName.setCombinationAuthorship(team);
+ }
+ if (taxonName.hasProblem()) {
+ logger.info("pb ICBN");
+ problem = true;
+ }
+ else {
+ return taxonName;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNB.getUuid())) {
+ NonViralName<BacterialName> taxonName = TaxonNameFactory.NewBacterialInstance(null);
+ taxonName.setFullTitleCache(fullName, true);
+ taxonName.setGenusOrUninomial(getFromMap(atomisedMap, "Genus"));
+ taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
+ taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "Species")));
+ taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "SubspeciesEpithet")));
+
+ if (taxonName.getGenusOrUninomial() != null){
+ taxonName.setRank(Rank.GENUS());
+ }
+ else if (taxonName.getInfraGenericEpithet() != null){
+ taxonName.setRank(Rank.SUBGENUS());
+ }
+ else if (taxonName.getSpecificEpithet() != null){
+ taxonName.setRank(Rank.SPECIES());
+ }
+ else if (taxonName.getInfraSpecificEpithet() != null){
+ taxonName.setRank(Rank.SUBSPECIES());
+ }
+
+ if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
+ Team team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
+ taxonName.setCombinationAuthorship(team);
+ }
+ if (getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear") != null) {
+ Team team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear"), true);
+ taxonName.setBasionymAuthorship(team);
+ }
+ if (taxonName.hasProblem()) {
+ logger.info("pb ICNB");
+ problem = true;
+ }
+ else {
+ return taxonName;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().equals("Cultivar")) {
+ CultivarPlantName taxonName = TaxonNameFactory.NewCultivarInstance(null);
+
+ if (taxonName.hasProblem()) {
+ logger.info("pb ICNCP");
+ problem = true;
+ }
+ else {
+ return taxonName;
+ }
+ return taxonName;
+ }
+
+ if (problem) {
+ logger.info("Problem im setTaxonNameByType ");
+ TaxonNameBase<?,?> taxonName = TaxonNameFactory.NewNonViralInstance(null);
+ taxonName.setFullTitleCache(fullName, true);
+ return taxonName;
+ }
+ TaxonNameBase<?,?> tn = TaxonNameFactory.NewNonViralInstance(null);
+ return tn;
+ }
+
+ /**
+ * Get a formated string from a hashmap
+ * @param atomisedMap
+ * @param key
+ * @return
+ */
+ private String getFromMap(HashMap<String, String> atomisedMap, String key) {
+ String value = null;
+ if (atomisedMap.containsKey(key)) {
+ value = atomisedMap.get(key);
+ }
+
+ try {
+ if (value != null && key.matches(".*Year.*")) {
+ value = value.trim();
+ if (value.matches("[a-z A-Z ]*[0-9]{4}$")) {
+ String tmp = value.split("[0-9]{4}$")[0];
+ int year = Integer.parseInt(value.split(tmp)[1]);
+ if (year >= 1752) {
+ value = tmp;
+ }
+ else {
+ value = null;
+ }
+ }
+ else {
+ value = null;
+ }
+ }
+ }
+ catch (Exception e) {
+ value = null;
+ }
+ return value;
+ }
+
+ /**
+ * Very fast and dirty implementation to allow handling of transient objects as described in
+ * https://dev.e-taxonomy.eu/trac/ticket/3726
+ *
+ * Not yet complete.
+ *
+ * @param cdmBase
+ * @param state
+ */
+ protected UUID save(CdmBase cdmBase, SpecimenImportStateBase state) {
+ ICdmApplicationConfiguration cdmRepository = state.getConfig().getCdmAppController();
+ if (cdmRepository == null){
+ cdmRepository = this;
+ }
+
+ if (cdmBase.isInstanceOf(LanguageString.class)){
+ return cdmRepository.getTermService().saveLanguageData(CdmBase.deproxy(cdmBase, LanguageString.class));
+ }else if (cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
+ return cdmRepository.getOccurrenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, SpecimenOrObservationBase.class));
+ }else if (cdmBase.isInstanceOf(Reference.class)){
+ return cdmRepository.getReferenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, Reference.class));
+ }else if (cdmBase.isInstanceOf(Classification.class)){
+ return cdmRepository.getClassificationService().saveOrUpdate(CdmBase.deproxy(cdmBase, Classification.class));
+ }else if (cdmBase.isInstanceOf(AgentBase.class)){
+ return cdmRepository.getAgentService().saveOrUpdate(CdmBase.deproxy(cdmBase, AgentBase.class));
+ }else if (cdmBase.isInstanceOf(Collection.class)){
+ return cdmRepository.getCollectionService().saveOrUpdate(CdmBase.deproxy(cdmBase, Collection.class));
+ }else if (cdmBase.isInstanceOf(DescriptionBase.class)){
+ return cdmRepository.getDescriptionService().saveOrUpdate(CdmBase.deproxy(cdmBase, DescriptionBase.class));
+ }else if (cdmBase.isInstanceOf(TaxonBase.class)){
+ return cdmRepository.getTaxonService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonBase.class));
+ }else if (cdmBase.isInstanceOf(TaxonNameBase.class)){
+ return cdmRepository.getNameService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonNameBase.class));
+ }else if (cdmBase.isInstanceOf(TaxonNode.class)){
+ return cdmRepository.getTaxonNodeService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonNode.class));
+ }else{
+ throw new IllegalArgumentException("Class not supported in save method: " + CdmBase.deproxy(cdmBase, CdmBase.class).getClass().getSimpleName());
+ }
+
+ }
+
+
+ protected SpecimenOrObservationBase findExistingSpecimen(String unitId, SpecimenImportStateBase state){
+ ICdmApplicationConfiguration cdmAppController = state.getConfig().getCdmAppController();
+ if(cdmAppController==null){
+ cdmAppController = this;
+ }
+ FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
+ config.setSignificantIdentifier(unitId);
+ Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
+ if(!existingSpecimens.getRecords().isEmpty()){
+ if(existingSpecimens.getRecords().size()==1){
+ return existingSpecimens.getRecords().iterator().next();
+ }
+ }
+ return null;
+ }
+
+ protected abstract void importAssociatedUnits(STATE state, Object item, DerivedUnitFacade derivedUnitFacade);
+
+ /**
+ * getFacade : get the DerivedUnitFacade based on the recordBasis
+ * @param state
+ *
+ * @return DerivedUnitFacade
+ */
+ protected DerivedUnitFacade getFacade(STATE state) {
+ if(DEBUG) {
+ logger.info("getFacade()");
+ }
+ SpecimenOrObservationType type = null;
+
+ // create specimen
+ if (NB((state.getDataHolder().getRecordBasis())) != null) {
+ if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("s") || state.getDataHolder().getRecordBasis().toLowerCase().indexOf("specimen")>-1) {// specimen
+ type = SpecimenOrObservationType.PreservedSpecimen;
+ }
+ if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("o") ||state.getDataHolder().getRecordBasis().toLowerCase().indexOf("observation")>-1 ) {
+ type = SpecimenOrObservationType.Observation;
+ }
+ if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("fossil")>-1){
+ type = SpecimenOrObservationType.Fossil;
+ }
+ if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("living")>-1) {
+ type = SpecimenOrObservationType.LivingSpecimen;
+ }
+ if (type == null) {
+ logger.info("The basis of record does not seem to be known: " + state.getDataHolder().getRecordBasis());
+ type = SpecimenOrObservationType.DerivedUnit;
+ }
+ // TODO fossils?
+ } else {
+ logger.info("The basis of record is null");
+ type = SpecimenOrObservationType.DerivedUnit;
+ }
+ DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(type);
+ return derivedUnitFacade;
+ }
+
+ /**
+ * Look if the Institution does already exist
+ * @param institutionCode: a string with the institutioncode
+ * @param config : the configurator
+ * @return the Institution (existing or new)
+ */
+ protected Institution getInstitution(String institutionCode, STATE state) {
+ SpecimenImportConfiguratorBase config = state.getConfig();
+ Institution institution=null;
+ institution = (Institution)state.institutions.get(institutionCode);
+ if (institution != null){
+ return institution;
+ }
+ List<Institution> institutions;
+ try {
+ institutions = getAgentService().searchInstitutionByCode(institutionCode);
+
+ } catch (Exception e) {
+ institutions = new ArrayList<Institution>();
+ logger.warn(e);
+ }
+ if (institutions.size() > 0 && config.isReuseExistingMetaData()) {
+ for (Institution institut:institutions){
+ try{
+ if (institut.getCode().equalsIgnoreCase(institutionCode)) {
+ institution=institut;
+ break;
+ }
+ }catch(Exception e){logger.warn("no institution code in the db");}
+ }
+ }
+ if(DEBUG) {
+ if(institution !=null) {
+ logger.info("getinstitution " + institution.toString());
+ }
+ }
+ if (institution == null){
+ // create institution
+ institution = Institution.NewInstance();
+ institution.setCode(institutionCode);
+ institution.setTitleCache(institutionCode, true);
+ UUID uuid = save(institution, state);
+ }
+
+
+ state.institutions.put(institutionCode, institution);
+ return institution;
+ }
+
+ /**
+ * Look if the Collection does already exist
+ * @param collectionCode
+ * @param collectionCode: a string
+ * @param config : the configurator
+ * @return the Collection (existing or new)
+ */
+ protected Collection getCollection(Institution institution, String collectionCode, STATE state) {
+ SpecimenImportConfiguratorBase config = state.getConfig();
+ Collection collection = null;
+ List<Collection> collections;
+ collection = (Collection) state.collections.get(collectionCode);
+ if (collection != null){
+ return collection;
+ }
+ try {
+ collections = getCollectionService().searchByCode(collectionCode);
+ } catch (Exception e) {
+ collections = new ArrayList<Collection>();
+ }
+ if (collections.size() > 0 && config.isReuseExistingMetaData()) {
+ for (Collection coll:collections){
+ if (coll.getCode() != null && coll.getInstitute() != null
+ && coll.getCode().equalsIgnoreCase(collectionCode) && coll.getInstitute().equals(institution)) {
+ collection = coll;
+ break;
+ }
+ }
+ }
+
+ if(collection == null){
+ collection =Collection.NewInstance();
+ collection.setCode(collectionCode);
+ collection.setInstitute(institution);
+ collection.setTitleCache(collectionCode);
+ UUID uuid = save(collection, state);
+ }
+
+
+
+ state.collections.put(collectionCode, collection);
+
+ return collection;
+ }
+
+ /**
+ * @param reference
+ * @param citationDetail
+ * @return
+ */
+ //FIXME this method is highly critical, because
+ // * it will have serious performance and memory problems with large databases
+ // (databases may easily have >1 Mio source records)
+ // * it does not make sense to search for existing sources and then clone them
+ // we need to search for existing references instead and use them (if exist)
+ // for our new source.
+ protected IdentifiableSource getIdentifiableSource(Reference reference, String citationDetail) {
+
+ /* List<IdentifiableSource> issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
+
+
+ if (reference != null){
+ try {
+ for (OriginalSourceBase<?> osb: issTmp){
+ if (osb.getCitation() != null && osb.getCitation().getTitleCache().equalsIgnoreCase(reference.getTitleCache())){
+ String osbDetail = osb.getCitationMicroReference();
+ if ((StringUtils.isBlank(osbDetail) && StringUtils.isBlank(citationDetail))
+ || (osbDetail != null && osbDetail.equalsIgnoreCase(citationDetail)) ) {
+// System.out.println("REFERENCE FOUND RETURN EXISTING SOURCE");
+ return (IdentifiableSource) osb.clone();
+ }
+ }
+ }
+ } catch (CloneNotSupportedException e) {
+ throw new RuntimeException(e);
+ } catch (Exception e1){
+ e1.printStackTrace();
+ }
+ }
+ */
+ IdentifiableSource sour = IdentifiableSource.NewInstance(OriginalSourceType.Import,null,null, reference,citationDetail);
+ return sour;
+ }
+
+ /**
+ * Add the hierarchy for a Taxon(add higher taxa)
+ * @param classification
+ * @param taxon: a taxon to add as a node
+ * @param state: the ABCD import state
+ */
+ protected void addParentTaxon(Taxon taxon, STATE state, boolean preferredFlag, Classification classification){
+ INonViralName nvname = taxon.getName();
+ Rank rank = nvname.getRank();
+ Taxon genus =null;
+ Taxon subgenus =null;
+ Taxon species = null;
+ Taxon subspecies = null;
+ Taxon parent = null;
+ if(rank!=null){
+ if (rank.isLower(Rank.GENUS() )){
+ String genusOrUninomial = nvname.getGenusOrUninomial();
+ TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(genusOrUninomial, Rank.GENUS(), preferredFlag, state, -1);
+ genus = getOrCreateTaxonForName(taxonName, state);
+ if (preferredFlag) {
+ parent = linkParentChildNode(null, genus, classification, state);
+ }
+
+ }
+ if (rank.isLower(Rank.SUBGENUS())){
+ String prefix = nvname.getGenusOrUninomial();
+ String name = nvname.getInfraGenericEpithet();
+ if (name != null){
+ TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SUBGENUS(), preferredFlag, state, -1);
+ subgenus = getOrCreateTaxonForName(taxonName, state);
+ if (preferredFlag) {
+ parent = linkParentChildNode(genus, subgenus, classification, state);
+ } }
+ }
+ if (rank.isLower(Rank.SPECIES())){
+ if (subgenus!=null){
+ String prefix = nvname.getGenusOrUninomial();
+ String name = nvname.getInfraGenericEpithet();
+ String spe = nvname.getSpecificEpithet();
+ if (spe != null){
+ TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(prefix+" "+name+" "+spe, Rank.SPECIES(), preferredFlag, state, -1);
+ species = getOrCreateTaxonForName(taxonName, state);
+ if (preferredFlag) {
+ parent = linkParentChildNode(subgenus, species, classification, state);
+ }
+ }
+ }
+ else{
+ String prefix = nvname.getGenusOrUninomial();
+ String name = nvname.getSpecificEpithet();
+ if (name != null){
+ TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SPECIES(), preferredFlag, state, -1);
+ species = getOrCreateTaxonForName(taxonName, state);
+ if (preferredFlag) {
+ parent = linkParentChildNode(genus, species, classification, state);
+ }
+ }
+ }
+ }
+ if (rank.isLower(Rank.INFRASPECIES())){
+ TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(nvname.getFullTitleCache(), Rank.SUBSPECIES(), preferredFlag, state, -1);
+ subspecies = getOrCreateTaxonForName(taxonName, state);
+ if (preferredFlag) {
+ parent = linkParentChildNode(species, subspecies, classification, state);
+ }
+ }
+ }
+ if (preferredFlag && parent!=taxon) {
+ linkParentChildNode(parent, taxon, classification, state);
+ }
+ }
+
+ /**
+ * Link a parent to a child and save it in the current classification
+ * @param parent: the higher Taxon
+ * @param child : the lower (or current) Taxon
+ * return the Taxon from the new created Node
+ * @param classification
+ * @param state
+ */
+ protected Taxon linkParentChildNode(Taxon parent, Taxon child, Classification classification, STATE state) {
+ TaxonNode node =null;
+ if (parent != null) {
+ parent = (Taxon) getTaxonService().find(parent.getUuid());
+ child = (Taxon) getTaxonService().find(child.getUuid());
+ //here we do not have to check if the taxon nodes already exists
+ //this is done by classification.addParentChild()
+ //do not add child node if it already exists
+ if(hasTaxonNodeInClassification(child, classification)){
+ return child;
+ }
+ else{
+ node = classification.addParentChild(parent, child, state.getRef(), "");
+ save(node, state);
+ }
+ }
+ else {
+ child = (Taxon) getTaxonService().find(child.getUuid());
+ //do not add child node if it already exists
+ if(hasTaxonNodeInClassification(child, classification)){
+ return child;
+ }
+ else{
+ node = classification.addChildTaxon(child, state.getRef(), null);
+ save(node, state);
+ }
+ }
+ if(node!=null){
+ state.getReport().addTaxonNode(node);
+ return node.getTaxon();
+ }
+ String message = "Could not create taxon node for " +child;
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ return null;
+ }
+
+ protected Taxon getOrCreateTaxonForName(TaxonNameBase<?, ?> taxonNameBase, STATE state){
+
+ Set<Taxon> acceptedTaxa = taxonNameBase.getTaxa();
+ if(acceptedTaxa.size()>0){
+ Taxon firstAcceptedTaxon = acceptedTaxa.iterator().next();
+ if(acceptedTaxa.size()>1){
+ String message = "More than one accepted taxon was found for taxon name: "
+ + taxonNameBase.getTitleCache() + "!\n" + firstAcceptedTaxon + "was chosen for "+state.getDerivedUnitBase();
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ }
+ else{
+ return firstAcceptedTaxon;
+ }
+ }
+ else{
+ Set<TaxonBase> taxonAndSynonyms = taxonNameBase.getTaxonBases();
+ for (TaxonBase taxonBase : taxonAndSynonyms) {
+ if(taxonBase.isInstanceOf(Synonym.class)){
+ Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
+ Taxon acceptedTaxonOfSynonym = synonym.getAcceptedTaxon();
+ if(acceptedTaxonOfSynonym == null){
+ String message = "No accepted taxon could be found for taxon name: "
+ + taxonNameBase.getTitleCache()
+ + "!";
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ }
+ else{
+ return acceptedTaxonOfSynonym;
+ }
+ }
+ }
+ }
+ Taxon taxon = Taxon.NewInstance(taxonNameBase, state.getRef());
+ save(taxon, state);
+ state.getReport().addTaxon(taxon);
+ logger.info("Created new taxon "+ taxon);
+ return taxon;
+ }
+
+ private boolean hasTaxonNodeInClassification(Taxon taxon, Classification classification){
+ if(taxon.getTaxonNodes()!=null){
+ for (TaxonNode node : taxon.getTaxonNodes()){
+ if(node.getClassification().equals(classification)){
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * HandleIdentifications : get the scientific names present in the ABCD
+ * document and store link them with the observation/specimen data
+ * @param state: the current ABCD import state
+ * @param derivedUnitFacade : the current derivedunitfacade
+ */
+ protected void handleIdentifications(STATE state, DerivedUnitFacade derivedUnitFacade) {
+ SpecimenImportConfiguratorBase config = state.getConfig();
+
+
+ String scientificName = "";
+ boolean preferredFlag = false;
+
+ if (state.getDataHolder().getNomenclatureCode() == ""){
+ if (config.getNomenclaturalCode() != null){
+ if (config.getNomenclaturalCode() != null){
+ state.getDataHolder().setNomenclatureCode(config.getNomenclaturalCode().toString());
+ }
+ }
+ }
+
+ for (int i = 0; i < state.getDataHolder().getIdentificationList().size(); i++) {
+ Identification identification = state.getDataHolder().getIdentificationList().get(i);
+ scientificName = identification.getScientificName().replaceAll(" et ", " & ");
+
+ String preferred = identification.getPreferred();
+ if (preferred.equals("1") || preferred.toLowerCase().indexOf("true") != -1 || state.getDataHolder().getIdentificationList().size()==1) {
+ preferredFlag = true;
+ }
+ else {
+ preferredFlag = false;
+ }
+ if (identification.getCode() != null){
+ if (identification.getCode().indexOf(':') != -1) {
+ state.getDataHolder().setNomenclatureCode(identification.getCode().split(COLON)[1]);
+ }
+ else{
+ state.getDataHolder().setNomenclatureCode(identification.getCode());
+ }
+ }
+ TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(scientificName, null, preferredFlag, state, i);
+ Taxon taxon = getOrCreateTaxonForName(taxonName, state);
+ addTaxonNode(taxon, state,preferredFlag);
+ linkDeterminationEvent(state, taxon, preferredFlag, derivedUnitFacade);
+ }
+ }
+
+ /**
+ * @param taxon : a taxon to add as a node
+ * @param state : the ABCD import state
+ */
+ protected void addTaxonNode(Taxon taxon, STATE state, boolean preferredFlag) {
+ SpecimenImportConfiguratorBase config = state.getConfig();
+ logger.info("link taxon to a taxonNode "+taxon.getTitleCache());
+ //only add nodes if not already existing in current classification or default classification
+
+ //check if node exists in current classification
+ //NOTE: we cannot use hasTaxonNodeInClassification() here because we are first creating it here
+ if (!existsInClassification(taxon,state.getClassification(), state)){
+ if(config.isMoveNewTaxaToDefaultClassification()){
+ //check if node exists in default classification
+ if (!existsInClassification(taxon, state.getDefaultClassification(), state)){
+ addParentTaxon(taxon, state, preferredFlag, state.getDefaultClassification());
+ }
+ }
+ else {
+ //add non-existing taxon to current classification
+ addParentTaxon(taxon, state, preferredFlag, state.getClassification());
+ }
+ }
+ }
+
+
+ private boolean existsInClassification(Taxon taxon, Classification classification, STATE state){
+ boolean exist = false;
+ ICdmApplicationConfiguration cdmAppController = state.getConfig().getCdmAppController();
+ if(cdmAppController==null){
+ cdmAppController = this;
+ }
+ if (classification != null){
+ List<UuidAndTitleCache<TaxonNode>> uuidAndTitleCacheOfAllTaxa = cdmAppController.getClassificationService().getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification.getUuid());
+ if (uuidAndTitleCacheOfAllTaxa != null){
+ for (UuidAndTitleCache p : uuidAndTitleCacheOfAllTaxa){
+ try{
+ if(p.getTitleCache().equals(taxon.getTitleCache())) {
+ exist = true;
+ }
+ }
+ catch(Exception e){
+ logger.warn("TaxonNode doesn't seem to have a taxon");
+ }
+ }
+ }
+ }
+ return exist;
+ }
+
+ /**
+ * join DeterminationEvent to the Taxon Object
+ * @param state : the ABCD import state
+ * @param taxon: the current Taxon
+ * @param preferredFlag :if the current name is preferred
+ * @param derivedFacade : the derived Unit Facade
+ */
+ @SuppressWarnings("rawtypes")
+ protected void linkDeterminationEvent(STATE state, Taxon taxon, boolean preferredFlag, DerivedUnitFacade derivedFacade) {
+ SpecimenImportConfiguratorBase config = state.getConfig();
+ if(DEBUG){
+ logger.info("start linkdetermination with taxon:" + taxon.getUuid()+", "+taxon);
+ }
+
+ DeterminationEvent determinationEvent = DeterminationEvent.NewInstance();
+ determinationEvent.setTaxonName(taxon.getName());
+ determinationEvent.setPreferredFlag(preferredFlag);
+
+ determinationEvent.setIdentifiedUnit(state.getDerivedUnitBase());
+ state.getDerivedUnitBase().addDetermination(determinationEvent);
+
+ if(DEBUG){
+ logger.info("NB TYPES INFO: "+ state.getDataHolder().getStatusList().size());
+ }
+ for (SpecimenTypeDesignationStatus specimenTypeDesignationstatus : state.getDataHolder().getStatusList()) {
+ if (specimenTypeDesignationstatus != null) {
+ if(DEBUG){
+ logger.info("specimenTypeDesignationstatus :"+ specimenTypeDesignationstatus);
+ }
+
+ ICdmApplicationConfiguration cdmAppController = config.getCdmAppController();
+ if(cdmAppController == null){
+ cdmAppController = this;
+ }
+ specimenTypeDesignationstatus = (SpecimenTypeDesignationStatus) cdmAppController.getTermService().find(specimenTypeDesignationstatus.getUuid());
+ //Designation
+ TaxonNameBase<?,?> name = taxon.getName();
+ SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance();
+
+ designation.setTypeStatus(specimenTypeDesignationstatus);
+ designation.setTypeSpecimen(state.getDerivedUnitBase());
+ name.addTypeDesignation(designation, true);
+ }
+ }
+
+ for (String[] fullReference : state.getDataHolder().getReferenceList()) {
+
+
+ String strReference=fullReference[0];
+ String citationDetail = fullReference[1];
+ String citationURL = fullReference[2];
+ List<Reference> references = getReferenceService().listByTitle(Reference.class, "strReference", MatchMode.EXACT, null, null, null, null, null);
+
+ if (!references.isEmpty()){
+ Reference reference = null;
+ for (Reference refe: references) {
+ if (refe.getTitleCache().equalsIgnoreCase(strReference)) {
+ reference =refe;
+ break;
+ }
+ }
+ if (reference ==null){
+ reference = ReferenceFactory.newGeneric();
+ reference.setTitleCache(strReference, true);
+ save(reference, state);
+ }
+ determinationEvent.addReference(reference);
+ }
+ }
+ save(state.getDerivedUnitBase(), state);
+
+ if (config.isAddIndividualsAssociationsSuchAsSpecimenAndObservations() && preferredFlag) {
+ //do not add IndividualsAssociation to non-preferred taxa
+ if(DEBUG){
+ logger.info("isDoCreateIndividualsAssociations");
+ }
+
+ makeIndividualsAssociation(state, taxon, determinationEvent);
+
+ save(state.getDerivedUnitBase(), state);
+ }
+ }
+
+ /**
+ * create and link each association (specimen, observation..) to the accepted taxon
+ * @param state : the ABCD import state
+ * @param taxon: the current Taxon
+ * @param determinationEvent:the determinationevent
+ */
+ protected void makeIndividualsAssociation(STATE state, Taxon taxon, DeterminationEvent determinationEvent) {
+ SpecimenImportConfiguratorBase config = state.getConfig();
+ SpecimenUserInteraction sui = config.getSpecimenUserInteraction();
+
+ if (DEBUG) {
+ logger.info("MAKE INDIVIDUALS ASSOCIATION");
+ }
+
+ TaxonDescription taxonDescription = null;
+ Set<TaxonDescription> descriptions= taxon.getDescriptions();
+// if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
+// if(!state.isDescriptionGroupSet()){
+// taxonDescription = sui.askForDescriptionGroup(descriptions);
+// state.setDescriptionGroup(taxonDescription);
+// state.setDescriptionGroupSet(true);
+// }else{
+// taxonDescription=state.getDescriptionGroup();
+// }
+// } else {
+ for (TaxonDescription description : descriptions){
+ Set<IdentifiableSource> sources = new HashSet<>();
+ sources.addAll(description.getTaxon().getSources());
+ sources.addAll(description.getSources());
+ for (IdentifiableSource source:sources){
+ if(state.getRef().equals(source.getCitation())) {
+ taxonDescription = description;
+ }
+ }
+ }
+ // }
+ if (taxonDescription == null){
+ taxonDescription = TaxonDescription.NewInstance(taxon, false);
+ if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
+ taxonDescription.addSource(OriginalSourceType.Import, null, null, state.getRef(), null);
+ }
+ state.setDescriptionGroup(taxonDescription);
+ taxon.addDescription(taxonDescription);
+ }
+
+ //PREPARE REFERENCE QUESTIONS
+
+ Map<String,OriginalSourceBase<?>> sourceMap = new HashMap<String, OriginalSourceBase<?>>();
+
+ List<IdentifiableSource> issTmp = new ArrayList<>();//getCommonService().list(IdentifiableSource.class, null, null, null, null);
+ List<DescriptionElementSource> issTmp2 = new ArrayList<>();//getCommonService().list(DescriptionElementSource.class, null, null, null, null);
+
+ Set<OriginalSourceBase> osbSet = new HashSet<OriginalSourceBase>();
+ if(issTmp2!=null) {
+ osbSet.addAll(issTmp2);
+ }
+ if(issTmp!=null) {
+ osbSet.addAll(issTmp);
+ }
+
+
+ addToSourceMap(sourceMap, osbSet);
+
+// if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
+// List<OriginalSourceBase<?>> res = null;
+// if(!state.isDescriptionSourcesSet()){
+// res = sui.askForSource(sourceMap, "the description group ("+taxon+")",
+// "The current reference is "+state.getRef().getTitleCache(),getReferenceService(), state.getDataHolder().docSources);
+// state.setDescriptionRefs(res);
+// state.setDescriptionSourcesSet(true);
+// }
+// else{
+// res=state.getDescriptionRefs();
+// }
+// if(res !=null) {
+// for (OriginalSourceBase<?> sour:res){
+// if(sour.isInstanceOf(IdentifiableSource.class)){
+// try {
+// if(sourceNotLinkedToElement(taxonDescription,sour)) {
+// taxonDescription.addSource((IdentifiableSource)sour.clone());
+// }
+// } catch (CloneNotSupportedException e) {
+// logger.warn("no cloning?");
+// }
+// }else{
+// if(sourceNotLinkedToElement(taxonDescription,sour)) {
+// taxonDescription.addSource(OriginalSourceType.Import,null, null, sour.getCitation(),sour.getCitationMicroReference());
+// }
+// }
+// }
+// }
+// }
+// else {
+ if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
+ taxonDescription.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
+ }
+// }
+ state.setDescriptionGroup(taxonDescription);
+
+ IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();
+ Feature feature = makeFeature(state.getDerivedUnitBase());
+ indAssociation.setAssociatedSpecimenOrObservation(state.getDerivedUnitBase());
+ indAssociation.setFeature(feature);
+//
+// if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
+// sourceMap = new HashMap<String, OriginalSourceBase<?>>();
+//
+// issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
+// issTmp2 = getCommonService().list(DescriptionElementSource.class, null, null, null, null);
+//
+// osbSet = new HashSet<OriginalSourceBase>();
+// if(issTmp2!=null) {
+// osbSet.addAll(issTmp2);
+// }
+// if(issTmp!=null) {
+// osbSet.addAll(issTmp);
+// }
+//
+//
+// addToSourceMap(sourceMap, osbSet);
+//
+// List<OriginalSourceBase<?>> sources =null;
+// if(!state.isAssociationSourcesSet()) {
+// sources = sui.askForSource(sourceMap, "descriptive element (association) ",taxon.toString(),
+// getReferenceService(),state.getDataHolder().getDocSources());
+// state.setAssociationRefs(sources);
+// state.setAssociationSourcesSet(true);
+// }
+// else{
+// sources=state.getAssociationRefs();
+// }
+// if(sources !=null) {
+// for (OriginalSourceBase<?> source: sources) {
+// if(source !=null) {
+// if(source.isInstanceOf(DescriptionElementSource.class)){
+// try {
+// if(sourceNotLinkedToElement(indAssociation,source)) {
+// indAssociation.addSource((DescriptionElementSource)source.clone());
+// }
+// } catch (CloneNotSupportedException e) {
+// logger.warn("clone forbidden?");
+// }
+// }else{
+// if(sourceNotLinkedToElement(indAssociation,source)) {
+// indAssociation.addSource(OriginalSourceType.Import,null, null, source.getCitation(),source.getCitationMicroReference());
+// }
+// try {
+// if(sourceNotLinkedToElement(state.getDerivedUnitBase(), source)) {
+// state.getDerivedUnitBase().addSource((IdentifiableSource) source.clone());
+// }
+// } catch (CloneNotSupportedException e) {
+// // TODO Auto-generated catch block
+// e.printStackTrace();
+// }
+// }
+//
+// }
+// }
+// }
+// }else {
+ if(sourceNotLinkedToElement(indAssociation,state.getRef(),null)) {
+ indAssociation.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
+ }
+ if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getRef(),null)) {
+ state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
+ }
+ for (Reference citation : determinationEvent.getReferences()) {
+ if(sourceNotLinkedToElement(indAssociation,citation,null))
+ {
+ indAssociation.addSource(DescriptionElementSource.NewInstance(OriginalSourceType.Import, null, null, citation, null));
+ }
+ if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getRef(),null)) {
+ state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
+ }
+ }
+ // }
+
+ taxonDescription.addElement(indAssociation);
+
+ save(taxonDescription, state);
+ save(taxon, state);
+ state.getReport().addDerivate(state.getDerivedUnitBase(), config);
+ state.getReport().addIndividualAssociation(taxon, state.getDataHolder().getUnitID(), state.getDerivedUnitBase());
+ }
+
+ /**
+ * @param derivedUnitBase2
+ * @param ref2
+ * @param object
+ * @return
+ */
+ private boolean sourceNotLinkedToElement(DerivedUnit derivedUnitBase2, Reference b, String d) {
+ Set<IdentifiableSource> linkedSources = derivedUnitBase2.getSources();
+ for (IdentifiableSource is:linkedSources){
+ Reference a = is.getCitation();
+ String c = is.getCitationMicroReference();
+
+ boolean refMatch=false;
+ boolean microMatch=false;
+
+ try{
+ if (a==null && b==null) {
+ refMatch=true;
+ }
+ if (a!=null && b!=null) {
+ if (a.getTitleCache().equalsIgnoreCase(b.getTitleCache())) {
+ refMatch=true;
+ }
+ }
+ }catch(Exception e){}
+
+
+ try{
+ if (c==null && d==null) {
+ microMatch=true;
+ }
+ if(c!=null && d!=null) {
+ if(c.equalsIgnoreCase(d)) {
+ microMatch=true;
+ }
+ }
+ }
+ catch(Exception e){}
+
+ if (microMatch && refMatch) {
+ return false;
+ }
+
+
+ }
+ return true;
+ }
+
+ private <T extends OriginalSourceBase<?>> boolean sourceNotLinkedToElement(ISourceable<T> sourcable, Reference reference, String microReference) {
+ Set<T> linkedSources = sourcable.getSources();
+ for (T is:linkedSources){
+ Reference unitReference = is.getCitation();
+ String unitMicroReference = is.getCitationMicroReference();
+
+ boolean refMatch=false;
+ boolean microMatch=false;
+
+ try{
+ if (unitReference==null && reference==null) {
+ refMatch=true;
+ }
+ if (unitReference!=null && reference!=null) {
+ if (unitReference.getTitleCache().equalsIgnoreCase(reference.getTitleCache())) {
+ refMatch=true;
+ }
+ }
+ }catch(Exception e){}
+
+ try{
+ if (unitMicroReference==null && microReference==null) {
+ microMatch=true;
+ }
+ if(unitMicroReference!=null && microReference!=null) {
+ if(unitMicroReference.equalsIgnoreCase(microReference)) {
+ microMatch=true;
+ }
+ }
+ }
+ catch(Exception e){}
+
+ if (microMatch && refMatch) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * look for the Feature object (FieldObs, Specimen,...)
+ * @param unit : a specimen or obersvation base
+ * @return the corresponding Feature
+ */
+ private Feature makeFeature(SpecimenOrObservationBase<?> unit) {
+ SpecimenOrObservationType type = unit.getRecordBasis();
+
+
+
+ if (type.isFeatureObservation()){
+ return Feature.OBSERVATION();
+ }else if (type.isFeatureSpecimen()){
+ return Feature.SPECIMEN();
+ }else if (type == SpecimenOrObservationType.DerivedUnit){
+ return Feature.OBSERVATION();
+ // return getFeature("Specimen or observation");
+ }else{
+ String message = "Unhandled record basis '%s' for defining individuals association feature type. Use default.";
+ logger.warn(String.format(message, type.getMessage()));
+ return Feature.OBSERVATION();
+ // return getFeature("Specimen or observation");
+
+ }
+ }
+
- protected abstract void doInvoke(STATE state);
+ /**
+ * @param sourceMap
+ * @param osbSet
+ */
+ protected void addToSourceMap(Map<String, OriginalSourceBase<?>> sourceMap, Set<OriginalSourceBase> osbSet) {
+ for( OriginalSourceBase<?> osb:osbSet) {
+ if(osb.getCitation()!=null && osb.getCitationMicroReference() !=null && !osb.getCitationMicroReference().isEmpty()) {
+ try{
+ sourceMap.put(osb.getCitation().getTitleCache()+ "---"+osb.getCitationMicroReference(),osb);
+ }catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
+ } else if(osb.getCitation()!=null){
+ try{
+ sourceMap.put(osb.getCitation().getTitleCache(),osb);
+ }catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
+ }
+ }
+ }
-}
\ No newline at end of file
+}
BGBM BDI Projects / cdmlib.git / blobdiff