+// $Id$
+/**
+* Copyright (C) 2017 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.bogota;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.UUID;
+
+import org.apache.log4j.Logger;
+import org.joda.time.Partial;
+import org.springframework.stereotype.Component;
+
+import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
+import eu.etaxonomy.cdm.common.CdmUtils;
+import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper;
+import eu.etaxonomy.cdm.model.agent.AgentBase;
+import eu.etaxonomy.cdm.model.agent.Institution;
+import eu.etaxonomy.cdm.model.agent.Person;
+import eu.etaxonomy.cdm.model.agent.Team;
+import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
+import eu.etaxonomy.cdm.model.common.CdmBase;
+import eu.etaxonomy.cdm.model.common.DefinedTerm;
+import eu.etaxonomy.cdm.model.common.ExtensionType;
+import eu.etaxonomy.cdm.model.common.IdentifiableSource;
+import eu.etaxonomy.cdm.model.common.Language;
+import eu.etaxonomy.cdm.model.common.TimePeriod;
+import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
+import eu.etaxonomy.cdm.model.description.TaxonDescription;
+import eu.etaxonomy.cdm.model.location.Country;
+import eu.etaxonomy.cdm.model.location.NamedArea;
+import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
+import eu.etaxonomy.cdm.model.location.NamedAreaType;
+import eu.etaxonomy.cdm.model.location.Point;
+import eu.etaxonomy.cdm.model.location.ReferenceSystem;
+import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
+import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
+import eu.etaxonomy.cdm.model.name.TaxonName;
+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.reference.Reference;
+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.strategy.exceptions.UnknownCdmTypeException;
+import eu.etaxonomy.cdm.strategy.parser.DeterminationModifierParser;
+import eu.etaxonomy.cdm.strategy.parser.SpecimenTypeParser;
+import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
+
+/**
+ * @author a.mueller
+ * @date 21.04.2017
+ *
+ */
+@Component
+public class BogotaSpecimenImport<CONFIG extends BogotaSpecimenImportConfigurator>
+ extends SimpleExcelSpecimenImport<CONFIG> {
+
+ private static final long serialVersionUID = -884838817884874228L;
+ private static final Logger logger = Logger.getLogger(BogotaSpecimenImport.class);
+
+ private static final String COL_TAXON_UUID = "Platform Name ID = cdmID";
+ private static final String COL_VOUCHER_ID = "Voucher ID";
+
+ private static final String COL_FAMILY = "Family";
+ private static final String COL_GENUS = "Genus";
+ private static final String COL_SPECIFIC_EPI = "Specific Epithet";
+ private static final String COL_BASIONYM_AUTHOR = "Author in parenthesis";
+ private static final String COL_AUTHOR = "Author";
+ private static final String COL_IDENTIFIER = "Identifier";
+ private static final String COL_IDENTIFICATION_DATE = "Identification date";
+ private static final String COL_IDENTIFICATION_QUALIFIER = "Qualifier";
+ private static final String COL_TYPUS = "Type";
+ private static final String COL_IDENTIFICATION_HISTORY = "Identification history";
+ private static final String COL_COLLECTOR_VERBATIM = "Verbatim Collectors (Originalfeld JBB)";
+ private static final String COL_COLLECTOR_LASTNAME = "Primary Collector Last Name (Originalfeld JBB)";
+ private static final String COL_COLLECTOR_FIRSTNAME = "Primary Collector First Name Initial (Originalfeld JBB)";
+ private static final String COL_COLLECTOR_MIDDLENAME = "Primary Collector Middle Name Initial (Originalfeld JBB)";
+ private static final String COL_COLLECTOR_TYPE = "Primary collector type (Originalfeld JBB)";
+ private static final String COL_COLLECTOR_NUMBER = "Collector's No";
+ private static final String COL_COLLECTORS = "Collectors";
+ private static final String COL_COLLECTION_DATE_FROM = "Collection Date from";
+ private static final String COL_COLLECTION_DATE_TO = "Collection Date to";
+ private static final String COL_ALTITUDE_FROM = "Altitude Value from";
+ private static final String COL_ALTITUDE_TO = "Altitude Value to";
+ private static final String COL_ALTITUDE_UNIT = "Altitude Unit";
+ private static final String COL_LOCALITY = "Locality";
+ private static final String COL_LOCALITY_ID = "LocalityID";
+ private static final String COL_LATITUDE = "Latitude";
+ private static final String COL_LONGITUDE = "Longitude";
+ private static final String COL_ERROR_DISTANCE = "Error distance in m";
+ private static final String COL_COUNTRY = "Country";
+ private static final String COL_STATE_AREA = "State/Province/Greater Area";
+ private static final String COL_GEO_METHOD = "Geocode Method";
+ private static final String COL_HABITUS = "Habitus";
+ private static final String COL_COLLECTION = "[Series] Voucher location";
+
+ private static final UUID uuidAnonymous = UUID.fromString("2303f043-6e92-4afa-9082-7719e78a1c8a");
+ private static final UUID uuidBogota = UUID.fromString("95b6cb03-8452-4439-98bd-8c1aa3c1da4e");
+ private static final UUID uuidDefaultGeocodMethod = UUID.fromString("0983e680-b0ca-4e46-8df7-0f1d757a2e01");
+ private static final UUID uuidExtTypeIdentificationHistory = UUID.fromString("7cee5c29-e16b-4e6f-ad57-bf7044259375");
+ private static final UUID uuidDetQualVelAff = UUID.fromString("511a0c23-2646-4035-b570-36bdc2eb5557");
+
+// @SuppressWarnings("unchecked")
+ private ImportDeduplicationHelper<SimpleExcelSpecimenImportState<?>> deduplicationHelper;
+// = (ImportDeduplicationHelper<SimpleExcelSpecimenImportState<?>>)ImportDeduplicationHelper.NewStandaloneInstance();
+
+
+ @Override
+ protected String getWorksheetName() {
+ return "To be imported";
+ }
+
+// private boolean isFirst = true;
+// private TransactionStatus tx = null;
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ protected void firstPass(SimpleExcelSpecimenImportState<CONFIG> state) {
+// if (isFirst){
+// tx = this.startTransaction();
+// isFirst = false;
+// }
+
+ HashMap<String, String> record = state.getOriginalRecord();
+
+ String voucherId = getValue(record, COL_VOUCHER_ID);
+ if (!isInInterval(state)){
+ return;
+ }
+ String line = state.getCurrentLine() + " (id:"+ voucherId+"): ";
+ if (state.getCurrentLine() % 100 == 0){System.out.println(line);}
+ try {
+
+ //species
+ TaxonBase<?> taxonBase = getOrCreateTaxon(state, line, record, voucherId);
+
+ if (taxonBase != null){
+ Taxon taxon = getTaxon(taxonBase);
+
+ TaxonDescription taxonDescription = getTaxonDescription(state, line, taxon);
+
+ DerivedUnit specimen = makeSpecimen(state, line, record, voucherId, taxonBase);
+
+ IndividualsAssociation indAssoc = IndividualsAssociation.NewInstance(specimen);
+ indAssoc.addImportSource(voucherId, COL_VOUCHER_ID, getSourceCitation(state), null);
+ taxonDescription.addElement(indAssoc);
+
+ }
+ } catch (Exception e) {
+ state.getResult().addError("An unexpected exception appeared in record", e, null, line);
+ e.printStackTrace();
+ }
+
+ }
+
+
+ /**
+ * @param state
+ * @return
+ */
+ private boolean isInInterval(SimpleExcelSpecimenImportState<CONFIG> state) {
+ Integer min = state.getConfig().getMinLineNumber();
+ Integer max = state.getConfig().getMaxLineNumber();
+ Integer current = state.getCurrentLine();
+ if (current < min || current > max){
+ return false;
+ }else{
+ return true;
+ }
+ }
+
+
+ /**
+ * @param state
+ * @param line
+ * @param taxon
+ * @return
+ */
+ private TaxonDescription getTaxonDescription(SimpleExcelSpecimenImportState<CONFIG> state, String line,
+ Taxon taxon) {
+ Reference ref = getSourceCitation(state);
+ TaxonDescription desc = this.getTaxonDescription(taxon, ref, ! IMAGE_GALLERY, CREATE);
+ return desc;
+ }
+
+
+ /**
+ * @param state
+ * @param line
+ * @param record
+ * @param voucherId
+ * @return
+ */
+ private DerivedUnit makeSpecimen(SimpleExcelSpecimenImportState<CONFIG> state, String line,
+ HashMap<String, String> record, String voucherId, TaxonBase<?> taxonBase) {
+
+ DerivedUnitFacade facade = DerivedUnitFacade.NewPreservedSpecimenInstance();
+ facade.setAccessionNumber(voucherId);
+ makeDetermination(facade.innerDerivedUnit(), state, line, record, taxonBase.getName());
+ makeTypus(facade.innerDerivedUnit(), state, line, record, taxonBase.getName());
+ makeCollectorFields(facade, state, line, record);
+ makeLocationFields(facade, state, line, record);
+ makeHabitus(facade, state, line, record);
+ makeCollection(facade, state, line, record);
+ DerivedUnit specimen = facade.innerDerivedUnit();
+ specimen.addSource(makeOriginalSource(state));
+ return specimen;
+ }
+
+
+ /**
+ * @param innerDerivedUnit
+ * @param state
+ * @param line
+ * @param record
+ * @param name
+ */
+ private void makeTypus(DerivedUnit specimen, SimpleExcelSpecimenImportState<CONFIG> state, String line,
+ HashMap<String, String> record, TaxonName name) {
+ String typus = record.get(COL_TYPUS);
+ if (typus != null){
+ SpecimenTypeDesignationStatus status;
+ try {
+ status = SpecimenTypeParser.parseSpecimenTypeStatus(typus);
+ SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance();
+ designation.setTypeStatus(status);
+ name.addSpecimenTypeDesignation(specimen, status, null, null, null, false, false);
+ } catch (UnknownCdmTypeException e) {
+ state.getResult().addWarning("Type designation could not be parsed", null, line);
+ }
+ }
+ }
+
+
+ /**
+ * @param facade
+ * @param state
+ * @param line
+ * @param record
+ */
+ private void makeCollection(DerivedUnitFacade facade, SimpleExcelSpecimenImportState<CONFIG> state,
+ String line, HashMap<String, String> record) {
+ String strCollection = record.get(COL_COLLECTION);
+ String collectionFormat = ".*\\([A-Z]{2,4}\\)";
+ if (!strCollection.matches(collectionFormat)){
+ String message = "Voucher location format does not match the expected format. Voucher '(" + strCollection + ")' location not added.";
+ state.getResult().addError(message, null, line);
+ return;
+ }
+ String[] splits = strCollection.split("\\(");
+ String collectionName = splits[0];
+ String collectionCode = splits[1].replace(")", "");
+ Collection collection = Collection.NewInstance();
+ collection.setName(collectionName);
+ collection.setCode(collectionCode);
+ collection = getDeduplicationHelper(state).getExistingCollection(state, collection);
+ facade.setCollection(collection);
+ }
+
+
+ /**
+ * @param state
+ * @return
+ */
+ private ImportDeduplicationHelper<SimpleExcelSpecimenImportState<?>> getDeduplicationHelper(SimpleExcelSpecimenImportState<CONFIG> state) {
+ if (deduplicationHelper == null){
+ deduplicationHelper = ImportDeduplicationHelper.NewInstance(this, state);
+ }
+ return deduplicationHelper;
+ }
+
+
+ /**
+ * @param facade
+ * @param state
+ * @param line
+ * @param record
+ */
+ private void makeHabitus(DerivedUnitFacade facade, SimpleExcelSpecimenImportState<CONFIG> state, String line,
+ HashMap<String, String> record) {
+ String habitus = record.get(COL_HABITUS);
+ if (habitus != null){
+ facade.setPlantDescription(habitus);
+ }
+ }
+
+
+ /**
+ * @param facade
+ * @param state
+ * @param line
+ * @param record
+ * @param voucherId
+ */
+ private void makeLocationFields(DerivedUnitFacade facade, SimpleExcelSpecimenImportState<CONFIG> state, String line,
+ HashMap<String, String> record) {
+ //Altitude
+ String strAltitudeFrom = record.get(COL_ALTITUDE_FROM);
+ String strAltitudeTo = record.get(COL_ALTITUDE_TO);
+ Integer intAltitudeFrom = intFromString(state, strAltitudeFrom, line, COL_ALTITUDE_FROM);
+ Integer intAltitudeTo = intFromString(state, strAltitudeTo, line, COL_ALTITUDE_TO);
+ if (intAltitudeFrom != null){
+ facade.setAbsoluteElevation(intAltitudeFrom);
+ if (!intAltitudeFrom.equals(intAltitudeTo)){
+ facade.setAbsoluteElevationMax(intAltitudeTo);
+ }
+ if (!record.get(COL_ALTITUDE_UNIT).equals("m")){
+ state.getResult().addWarning("Altitude unit is not m but " + record.get(COL_ALTITUDE_UNIT), "makeLocationFields", line);
+ }
+ }
+ checkNoToIfNoFrom(strAltitudeFrom, strAltitudeTo, state, line, COL_ALTITUDE_TO);
+
+ //locality
+ String locality = record.get(COL_LOCALITY);
+ if (locality != null){ //should always exist
+ facade.setLocality(locality, Language.SPANISH_CASTILIAN());
+ }
+
+ //Lat + Long
+ String strLatitude = record.get(COL_LATITUDE);
+ String strLongitude = record.get(COL_LONGITUDE);
+ String strError = record.get(COL_ERROR_DISTANCE);
+ Double dblLatitude = doubleFromString(state, strLatitude, line, COL_LATITUDE);
+ Double dblLongitude = doubleFromString(state, strLongitude, line, COL_LONGITUDE);
+ Integer intError = intFromString(state, strError, line, COL_ERROR_DISTANCE);
+ ReferenceSystem referenceSystem = makeReferenceSystem(state, record, line);
+
+ if (dblLatitude != null || dblLongitude != null || intError != null){ //should always exist
+ Point exactLocation = Point.NewInstance(dblLongitude, dblLatitude, referenceSystem, intError);
+ facade.setExactLocation(exactLocation);
+ }
+
+ //Country
+ String strCountry = record.get(COL_COUNTRY);
+ if (strCountry != null){
+ if (strCountry.equals("Colombia")){
+ Country colombia = Country.COLOMBIAREPUBLICOF();
+ colombia.setLabel("Colombia");
+ getTermService().saveOrUpdate(colombia);
+ facade.setCountry(colombia);
+ }else{
+ state.getResult().addWarning("Country was not Colombia as expected but " + strCountry,
+ "makeLocationFields", line);
+ }
+ }
+
+ //State
+ String strStateArea = record.get(COL_STATE_AREA);
+ if (strStateArea != null){
+ if (strStateArea.replaceAll("\\s", "").equalsIgnoreCase("Bogotá,D.C.")){
+ NamedArea bogota = makeBogota(state, line);
+ facade.addCollectingArea(bogota);
+ }else{
+ state.getResult().addWarning(COL_STATE_AREA + " was not 'Bogotá, D.C.' as expected but " + strCountry,
+ "makeLocationFields", line);
+ }
+ }
+ }
+
+
+ /**
+ * @param strAltitudeFrom
+ * @param strAltitudeTo
+ * @param state
+ * @param line
+ * @param colAltitudeTo
+ */
+ private void checkNoToIfNoFrom(String strFrom, String strTo,
+ SimpleExcelSpecimenImportState<CONFIG> state,
+ String line, String toAttributeName) {
+ if (isNotBlank(strTo) && isBlank(strFrom)){
+ String message = "A min-max attribute has a max value (%s) but no min value. This is invalid."
+ + " The max value attribute name is %s.";
+ message = String.format(message, strTo, toAttributeName);
+ state.getResult().addWarning(message, null, line);
+ }
+ }
+
+ private ReferenceSystem defaultGeocodeMethod;
+
+ /**
+ * @param state
+ * @param record
+ * @param line
+ * @return
+ */
+ private ReferenceSystem makeReferenceSystem(SimpleExcelSpecimenImportState<CONFIG> state,
+ Map<String, String> record, String line) {
+ String defaultStrRefSys = "Wieczorek, J., Guo, Q., & Hijmans, R. (2004). The point-radius method for georeferencing locality descriptions and calculating associated uncertainty. International journal of geographical information science, 18(8), 745-767.; Escobar D, Díaz SR, Jojoa LM, Rudas E, Albarracín RD, Ramírez C, Gómez JY, López CR, Saavedra J (2015). Georreferenciación de localidades: Una guía de referencia para colecciones biológicas. Instituto de Investigación de Recursos Biológicos Alexander von Humboldt – Instituto de Ciencias Naturales, Universidad Nacional de Colombia. Bogotá D.C., Colombia. 95 p.";
+ String strRefSys = record.get(COL_GEO_METHOD);
+ if (strRefSys == null){
+ return null;
+ }else if (!strRefSys.equals(defaultStrRefSys)){
+ state.getResult().addError("The expected Geocode Method is not the expected default method. Geocode Method was not added.", null, line);
+ return null;
+ }else if (defaultGeocodeMethod != null){
+ return defaultGeocodeMethod;
+ }else{
+ String label = "Point radius method";
+ String description = defaultStrRefSys;
+ String labelAbbrev = "PRM";
+ defaultGeocodeMethod = getReferenceSystem(state, uuidDefaultGeocodMethod,
+ label, description, labelAbbrev, null);
+ return defaultGeocodeMethod;
+ }
+ }
+
+ private NamedArea bogota;
+ /**
+ * @param state
+ * @param line
+ * @return
+ */
+ private NamedArea makeBogota(SimpleExcelSpecimenImportState<CONFIG> state, String line) {
+ if (bogota != null){
+ return bogota;
+ }else{
+ String label = "Bogotá, D.C.";
+ NamedAreaType areaType = NamedAreaType.ADMINISTRATION_AREA();
+ NamedAreaLevel level = NamedAreaLevel.STATE();
+ bogota = getNamedArea(state, uuidBogota, label, label, null, areaType,
+ level, null, null, null);
+ return bogota;
+ }
+ }
+
+
+ /**
+ * @param facade
+ * @param state
+ * @param line
+ * @param record
+ */
+ private void makeCollectorFields(DerivedUnitFacade facade, SimpleExcelSpecimenImportState<CONFIG> state, String line,
+ HashMap<String, String> record) {
+
+ //collector number
+ facade.setFieldNumber(record.get(COL_COLLECTOR_NUMBER));
+
+ //gathering date
+ String dateFrom = unknownToNull((record.get(COL_COLLECTION_DATE_FROM)));
+ String dateTo = unknownToNull(record.get(COL_COLLECTION_DATE_TO));
+ checkNoToIfNoFrom(dateFrom, dateTo, state, line, COL_COLLECTION_DATE_TO);
+ try {
+ if (dateFrom != null && dateFrom.equals(dateTo)){
+ dateTo = null;
+ }
+ TimePeriod gatheringPeriod = TimePeriodParser.parseEnglishDate(dateFrom, dateTo);
+ facade.setGatheringPeriod(gatheringPeriod);
+ } catch (Exception e) {
+ state.getResult().addError("Error creating gathering date", e, null, line);
+ }
+
+ //collector
+ String collectorType = record.get(COL_COLLECTOR_TYPE);
+ String collectors = record.get(COL_COLLECTORS);
+ AgentBase<?> collector;
+ if (collectorType.startsWith("Anonymous")){
+ collector = getAnonymous();
+ }else if (collectorType.equals("Brother") || collectorType.equals("Person")){
+ Person person = Person.NewInstance();
+ if (collectorType.equals("Person")){
+ person.setLastname(record.get(COL_COLLECTOR_LASTNAME));
+ String initials = CdmUtils.concat("", record.get(COL_COLLECTOR_FIRSTNAME), record.get(COL_COLLECTOR_MIDDLENAME));
+ initials = (initials == null)? null : initials.replaceAll("\\s", "");
+ person.setInitials(initials);
+ String full = person.getTitleCache();
+ if (!full.equals(collectors)){
+ person.setTitleCache(collectors, true);
+ //TODO longterm, collector cache
+ }
+ }else{
+ person.setTitleCache(collectors, true);
+ person.setPrefix("Hno.");
+ person.setFirstname(collectors.replace("Hno.", "").trim());
+ }
+ collector = person;
+ }else if (collectorType.equals("Group")){
+ collector = Team.NewTitledInstance(collectors, collectors);
+ }else if (collectorType.equals("Institution")){
+ collector = Institution.NewNamedInstance(collectors);
+ }else{
+ String message = "Collector type " + collectorType + " not yet supported by import. Collector not added.";
+ state.getResult().addError(message, null, line);
+ collector = null;
+ }
+ collector = getDeduplicationHelper(state).getExistingAgent(state, collector);
+ facade.setCollector(collector);
+ }
+
+
+ /**
+ * @param string
+ * @return
+ */
+ private String unknownToNull(String string) {
+ if (string == null || string.equalsIgnoreCase("unknown")){
+ return null;
+ }else{
+ return string;
+ }
+ }
+
+ private Person anonymous;
+ private Person getAnonymous() {
+ if (anonymous != null){
+ return anonymous;
+ }
+ anonymous = CdmBase.deproxy(getAgentService().find(uuidAnonymous), Person.class);
+ if (anonymous == null){
+ anonymous = Person.NewTitledInstance("Anon.");
+ anonymous.setUuid(uuidAnonymous);
+ getAgentService().save(anonymous);
+ }
+ return anonymous;
+ }
+
+
+ /**
+ * @param facade
+ * @param state
+ * @param line
+ * @param record
+ * @param taxonBase
+ */
+ private void makeDetermination(DerivedUnit specimen, SimpleExcelSpecimenImportState<CONFIG> state, String line,
+ HashMap<String, String> record, TaxonName taxonName) {
+
+ DeterminationEvent determination;
+ determination = DeterminationEvent.NewInstance(taxonName, specimen);
+ determination.setPreferredFlag(true);
+
+ //determiner/identifier
+ TeamOrPersonBase<?> determiner = makeDeterminer(state, record, line);
+ determination.setDeterminer(determiner);
+
+ //date
+ TimePeriod date = makeIdentificationDate(state, record, line);
+ determination.setTimeperiod(date);
+
+ //qualifier
+ DefinedTerm qualifier = makeDeterminationQualifier(state, record, line);
+ determination.setModifier(qualifier);
+
+ //history
+ String history = record.get(COL_IDENTIFICATION_HISTORY);
+ if (history != null){
+ String label = "Identification History";
+ String text = label;
+ ExtensionType detHistoryType = getExtensionType(state, uuidExtTypeIdentificationHistory, label, text, null);
+ specimen.addExtension(history, detHistoryType);
+ }
+ }
+
+
+ /**
+ * @param state
+ * @param record
+ * @param line
+ * @return
+ */
+ private TeamOrPersonBase<?> makeDeterminer(SimpleExcelSpecimenImportState<CONFIG> state,
+ HashMap<String, String> record, String line) {
+ String identifier = record.get(COL_IDENTIFIER);
+ if (identifier == null){
+ return null;
+ }else if (identifier.equals("Anon.")){
+ return getAnonymous();
+ }else{
+ Person person = Person.NewInstance();
+ person.setTitleCache(identifier, true);
+// String format = "([A-Z]\\.){1,3}" +
+// NonViralNameParserImplRegExBase.capitalWord +
+// "(-" + NonViralNameParserImplRegExBase.capitalWord;
+
+ String[] splits = identifier.split("\\.");
+ int length = splits.length;
+ if (splits[length - 1].equals("")){
+ splits[length - 2]= splits[length - 2]+".";
+ length--;
+ }
+ if (splits[length - 1].startsWith("-")){
+ splits[length - 2]= splits[length - 2]+"." + splits[length - 1];
+ length--;
+ }
+ String lastName = splits[length - 1];
+ String initials = null;
+ for (int i= 0; i < length-1;i++){
+ initials = CdmUtils.concat("", initials, splits[i]+".");
+ }
+ person.setLastname(lastName);
+ person.setInitials(initials);
+ TeamOrPersonBase<?> result = getDeduplicationHelper(state).getExistingAuthor(state, person);
+ return result;
+ }
+ }
+
+
+ /**
+ * @param state
+ * @param record
+ * @param line
+ * @return
+ */
+ private TimePeriod makeIdentificationDate(SimpleExcelSpecimenImportState<CONFIG> state,
+ HashMap<String, String> record, String line) {
+ String strDate = record.get(COL_IDENTIFICATION_DATE);
+ if (strDate == null || strDate.equals("s.n.")){
+ return null;
+ }
+ String[] splits = strDate.split("/");
+ String strYear = splits[splits.length-1];
+ String strMonth = splits.length < 2? null:splits[splits.length-2];
+ String strDay = splits.length < 3? null:splits[splits.length-3];
+
+ Integer year = intFromString(state, strYear, line, COL_IDENTIFICATION_DATE);
+ Integer month = intFromString(state, strMonth, line, COL_IDENTIFICATION_DATE);
+ Integer day = intFromString(state, strDay, line, COL_IDENTIFICATION_DATE);
+ Partial start = TimePeriodParser.makePartialFromDateParts(year, month, day);
+ return TimePeriod.NewInstance(start);
+ }
+
+
+ /**
+ * @param state
+ * @param record
+ * @param line
+ * @return
+ */
+ private DefinedTerm makeDeterminationQualifier(SimpleExcelSpecimenImportState<CONFIG> state,
+ HashMap<String, String> record, String line) {
+ String qualifier = record.get(COL_IDENTIFICATION_QUALIFIER);
+ if (qualifier != null){
+ try {
+ return DeterminationModifierParser.parseDeterminationQualifier(qualifier);
+ } catch (UnknownCdmTypeException e) {
+ //TODO add to terms
+ if (qualifier.equals("vel. aff.")){
+
+ DefinedTerm velAff = (DefinedTerm)getTermService().find(uuidDetQualVelAff);
+ if (velAff == null){
+ velAff = DefinedTerm.NewModifierInstance(qualifier, qualifier, qualifier);
+ velAff.setUuid(uuidDetQualVelAff);
+ getTermService().save(velAff);
+ }
+ return velAff;
+ }
+ state.getResult().addError("Determination qualifier could not be recognized: " + qualifier, null, line);
+ return null;
+ }
+ }else{
+ return null;
+ }
+ }
+
+
+ /**
+ * @param taxonBase
+ * @return
+ */
+ private Taxon getTaxon(TaxonBase<?> taxonBase) {
+ if (taxonBase.isInstanceOf(Synonym.class)){
+ return CdmBase.deproxy(taxonBase, Synonym.class).getAcceptedTaxon();
+ }else{
+ return CdmBase.deproxy(taxonBase, Taxon.class);
+ }
+ }
+
+
+ /**
+ * @param state
+ * @param line
+ * @param record
+ * @param noStr
+ * @return
+ */
+ private TaxonBase<?> getOrCreateTaxon(SimpleExcelSpecimenImportState<CONFIG> state, String line,
+ HashMap<String, String> record, String noStr) {
+
+ String strUuidTaxon = record.get(COL_TAXON_UUID);
+ if (strUuidTaxon != null){
+ UUID uuidTaxon;
+ try {
+ uuidTaxon = UUID.fromString(strUuidTaxon);
+ } catch (Exception e) {
+ state.getResult().addError("Taxon uuid has incorrect format. Taxon could not be loaded. Data not imported.", null, line);
+ return null;
+ }
+ TaxonBase<?> result = getTaxonService().find(uuidTaxon);
+ if (result == null){
+ state.getResult().addError("Taxon for uuid "+strUuidTaxon+" could not be found in database. "
+ + "Taxon could not be loaded. Data not imported.", null, line);
+
+ }
+ return result;
+ }else{
+ TaxonName taxonName = null;
+ Reference sec = null;
+ Taxon result = Taxon.NewInstance(taxonName, sec);
+ result.addSource(makeOriginalSource(state));
+ //TODO export uuid
+
+// state.getResult().addInfo("Taxon");
+ //TODO
+ return null;
+ }
+ }
+
+
+ @Override
+ protected void secondPass(SimpleExcelSpecimenImportState<CONFIG> state) {
+// if (tx != null){
+// this.commitTransaction(tx);
+// tx = null;
+// }
+ }
+
+ @Override
+ protected IdentifiableSource makeOriginalSource(SimpleExcelSpecimenImportState<CONFIG> state) {
+ return IdentifiableSource.NewDataImportInstance(getValue(state.getOriginalRecord(), COL_VOUCHER_ID), COL_VOUCHER_ID, getSourceCitation(state));
+ }
+
+ /**
+ * @param state
+ * @return
+ */
+ protected Reference getSourceCitation(SimpleExcelSpecimenImportState<CONFIG> state) {
+ Reference source = state.getConfig().getSourceReference();
+ if (source.getId() == 0){
+ Reference persisted = getReferenceService().find(source.getUuid());
+ if (persisted == null){
+ getReferenceService().saveOrUpdate(source);
+ }else{
+ state.getConfig().setSourceReference(persisted);
+ source = persisted;
+ }
+ }
+ return source;
+ }
+}
BGBM BDI Projects / cdmlib-apps.git / commitdiff