EDIT

/**

* Copyright (C) 2007 EDIT

* 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.

*/

 */

public class CaryoActivator extends SourceBase{

	private static final Logger logger = Logger.getLogger(CaryoActivator.class);

	//database validation status (create, update, validate ...)

	static final DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;

	static final Source source = caryo_len61();

	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest();

	static final String classificationName = "Caryophyllales";

	//classification

	static final UUID classificationUuid = UUID.fromString("9edc58b5-de3b-43aa-9f31-1ede7c009c2b");

	//check - import

	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	//taxa

	static final boolean doTaxa = true;

	static final boolean doDeduplicate = true;

	private void doImport(ICdmDataSource cdmDestination){

		//make Source

		CaryoImportConfigurator config= CaryoImportConfigurator.NewInstance(source, cdmDestination);

		config.setClassificationUuid(classificationUuid);

		config.setDbSchemaValidation(hbm2dll);

		config.setSourceReferenceTitle("NCU - Caryophyllales, v0.4");

		config.setClassificationName(classificationName);

		CdmDefaultImport<CaryoImportConfigurator> myImport = new CdmDefaultImport<CaryoImportConfigurator>();

		//...

		if (true){

			System.out.println("Start import from ("+ source.toString() + ") ...");

			myImport.invoke(config);

			System.out.println("End import from ("+ source.toString() + ")...");

		}

		//deduplicate

		if (doDeduplicate){

			ICdmApplicationConfiguration app = myImport.getCdmAppController();

			count = app.getReferenceService().deduplicate(Reference.class, null, null);

			logger.warn("Deduplicated " + count + " references.");

		}

	}

		result.setTitleCache(string);

		return result;

	}

		CaryoActivator me = new CaryoActivator();

		me.doImport(cdmDestination);

	}

}

import eu.etaxonomy.cdm.io.cuba.CubaImportConfigurator;

import eu.etaxonomy.cdm.io.cuba.CubaTransformer;

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

import eu.etaxonomy.cdm.model.description.Feature;

import eu.etaxonomy.cdm.model.description.FeatureNode;

import eu.etaxonomy.cdm.model.description.FeatureTree;

	private static final Logger logger = Logger.getLogger(CubaActivator.class);

	//database validation status (create, update, validate ...)

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();

    boolean doAsteraceae = include;

    boolean doConvolvulaceae = include;

	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	boolean doVocabularies = (hbm2dll == DbSchemaValidation.CREATE);

	private void doImport(ICdmDataSource cdmDestination){

        }

		//deduplicate

		if (doDeduplicate){

		    logger.warn("Start deduplication ...");

            }

			int count = app.getAgentService().deduplicate(Person.class, null, null);

			logger.warn("Deduplicated " + count + " persons.");

		}

		System.exit(0);

        System.out.println("End import from ("+ source.toString() + ")...");

    }

		result.setTitleCache(string, true);

		result.setInReference(inRef);

		inRef.setTitleCache(sourceReferenceTitle, true);

	}

		result.setTitleCache(string, true);

		return result;

	}

/**

* Copyright (C) 2007 EDIT

* 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.

*/

 */

public class CyprusAltitudeActivator {

	private static final Logger logger = Logger.getLogger(CyprusAltitudeActivator.class);

	//database validation status (create, update, validate ...)

	static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;

//	static final URI source = cyprus_distribution();

	static final URI source = cyprus_altitude();

	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_dev();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_production();

	//feature tree uuid

	public static final UUID featureTreeUuid = UUID.fromString("14d1e912-5ec2-4d10-878b-828788b70a87");

	//classification

	static final UUID classificationUuid = UUID.fromString("0c2b5d25-7b15-4401-8b51-dd4be0ee5cab");

	private static final String sourceReferenceTitle = "Cyprus Excel Altitude Import";

	//TODO move to Feature vocabulary

	private static final UUID uuidAltitudeFeature = UUID.fromString("1a28ed59-e15f-4001-b5c2-ea89f0012671");

	//check - import

	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	private void doImport(ICdmDataSource cdmDestination){

		ArrayList<HashMap<String, String>> excel;

		try {

			excel = ExcelUtils.parseXLS(source, "coreTax");

			e.printStackTrace();

			return;

		}

		CdmApplicationController app = CdmIoApplicationController.NewInstance(cdmDestination, hbm2dll);

		Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();

		TransactionStatus tx = app.startTransaction();

		UUID uuidMikle77 = UUID.fromString("9f5fa7ee-538b-4ae5-bd82-2a9503fea1d6");

		UUID uuidMikle85 = UUID.fromString("994403c4-c400-413d-9a1a-8531a40bfd8c");

		Feature altitudeFeature = (Feature) app.getTermService().find(uuidAltitudeFeature);

		if (altitudeFeature == null){

//			altitudeFeature = Feature.NewInstance("Altitude", "Altitude", "alt.");

//			featureVoc.addTerm(altitudeFeature);

			throw new RuntimeException("Could not find altitudinal range feature");

		}

		MeasurementUnit meter = (MeasurementUnit)app.getTermService().find(UUID.fromString("8bef5055-789c-41e5-bea2-8dc2ea8ecdf6"));

//		NamedArea cyprus = (NamedArea)app.getTermService().find(UUID.fromString("da4cce9a-439b-4cc4-8073-85dc75bae169"));

		int count =1;

		for (HashMap<String, String> row : excel){

			count++;

			UUID baseUuid = makeUuid(row, "uuid");

			UUID acceptedUuid = makeUuid(row, "acceptedNameUuid");

			UUID parentUuid = makeUuid(row, "parentUuid");

//			String altitude = row.get("Altitude-kumuliert");

			String altitudeMin = row.get("Min");

			String altitudeMax = row.get("Max");

			String acceptedName = row.get("AcceptedName");

			String source = row.get("Source");

			if (StringUtils.isBlank(altitudeMin)){

				continue;

			}

			boolean hasAltitude = false;

			Taxon taxon = getTaxon(app, baseUuid, acceptedUuid, parentUuid, acceptedName, count);

			if (taxon != null){

				TaxonDescription desc = getDescription(taxon, sourceRef);

				hasAltitude = makeAltitude(altitudeMin, altitudeMax, altitudeFeature, sourceRef, desc, meter, count);

//				hasAltitude = makeAltitudeOld(altitude, altitudeFeature, sourceRef, desc, meter, count);

				if (hasAltitude){

		}

		app.getTaxonService().saveOrUpdate(taxaToSave);

//		tx.setRollbackOnly();

		app.commitTransaction(tx);

	}

	private Taxon getTaxon(CdmApplicationController app, UUID baseUuid, UUID acceptedUuid, UUID parentUuid, String acceptedName, int row) {

		TaxonBase<?> base = app.getTaxonService().find(baseUuid);

//		TaxonBase<?> parent = app.getTaxonService().find(parentUuid);

		//TODO

		Taxon result = null;

		if (base.isInstanceOf(Taxon.class)){

				}else{

					logger.warn("Synonym relation has changed somehow. Row: " + row +  ", Taxon: " + base.getTitleCache());

				}

			}else{

				logger.warn("Accepted taxon not in classification. Row: " + row +  ", Taxon: " + base.getTitleCache());

			}

		}

		if (result != null){

			if (! result.getName().getTitleCache().equals(acceptedName)){

				logger.warn("AcceptedName and taxon name is not equal in " + row + ".\n" +

						" Taxon    Name: " + result.getName().getTitleCache());

			}

		}

		return result;

	}

//	private static final Pattern altitudePattern = Pattern.compile("\\d{1,4}(-\\d{1,4})?");

		QuantitativeData data = QuantitativeData.NewInstance(altitudeFeature);

		//Meikle

		if (source != null){

			TaxonNameBase<?,?> nameUsedInSource = null;  //TODO

//		//Excel   //excel source not wanted by Ralf

//		TaxonNameBase<?,?> nameUsedInSource = null;  //TODO probably we don't want this

//		data.addSource(OriginalSourceType.Import, String.valueOf(row), "row", getSourceReference(), null, nameUsedInSource, null);

		data.setUnit(meter);

		Integer min = Integer.valueOf(altitudeMin);

		StatisticalMeasurementValue minValue = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MIN(), min);

		data.addStatisticalValue(minValue);

		Integer max = Integer.valueOf(altitudeMax);

		StatisticalMeasurementValue maxValue = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MAX(), max);

		data.addStatisticalValue(maxValue);

		desc.addElement(data);

		return true;

	}

//		String altitude = altitudeOrig.trim().replace(" ", "");

//		Matcher matcher = altitudePattern.matcher(altitude);

//		if (matcher.matches()){

//			QuantitativeData data = QuantitativeData.NewInstance(feature);

//			//Meikle

//			if (source != null){

//				TaxonNameBase<?,?> nameUsedInSource = null;  //TODO

//			TaxonNameBase<?,?> nameUsedInSource = null;  //TODO probably we don't want this

//			data.addSource(OriginalSourceType.Import, String.valueOf(row), "row", getSourceReference(), null, nameUsedInSource, null);

//			data.setUnit(meter);

//			String[] split = altitude.split("-");

//

//			Integer min = Integer.valueOf(split[0]);

//		}

//	}

		if (taxon != null){

			//TODO Mikle existiert derzeit nicht also Source

			TaxonDescription desc = TaxonDescription.NewInstance();

			desc.setTitleCache("Import from " + getSourceReference().getTitleCache(), true);

			desc.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, sourceRef,null);

			desc.addSource(OriginalSourceType.Import, null, null, getSourceReference(), null);

			return desc;

		}

		return null;

	}

		if(StringUtils.isNotBlank(source)){

			if (source.equals("Meikle 1977")){

				return m77;

//		// TODO Auto-generated method stub

//		HashMap<String, Object> = new HashM

//		row

//	}

		if (sourceReference == null){

			sourceReference = ReferenceFactory.newGeneric();

			sourceReference.setTitleCache(sourceReferenceTitle, true);

		}

		return sourceReference;

	}

	//Cyprus

	public static URI cyprus_altitude() {

		URI sourceUrl;

	private void testMatcher() {

//		makeAltitude("0-4400", null, null);

	}

}

/**

* Copyright (C) 2007 EDIT

* 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.

*/

public class CyprusSpecimenActivator {

	@SuppressWarnings("unused")

	private static final Logger logger = Logger.getLogger(CyprusSpecimenActivator.class);

	//database validation status (create, update, validate ...)

	static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;

	static final URI source = cyprus_specimen_local();

//	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();

	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_dev();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_production();

	//check - import

	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	//taxa

//	static final boolean doTaxa = false;

//	static final boolean doDeduplicate = false;

//	static final boolean doDistribution = true;

	private void doImport(ICdmDataSource cdmDestination){

		//make Source

		SpecimenCdmExcelImportConfigurator config= SpecimenCdmExcelImportConfigurator.NewInstance(source, cdmDestination);

		config.setCheck(check);

		config.setDbSchemaValidation(hbm2dll);

		CdmDefaultImport myImport = new CdmDefaultImport();

		//...

		if (true){

			System.out.println("Start import from ("+ source.toString() + ") ...");

			System.out.println("End import from ("+ source.toString() + ")...");

		}

	}

		result.setTitleCache(string, true);

		return result;

	}

	//Cyprus

	public static URI cyprus_specimen_local() {

		URI sourceUrl;

		}

	}

	/**

	 * @param args

		CyprusSpecimenActivator me = new CyprusSpecimenActivator();

		me.doImport(cdmDestination);

	}

}

	}

		result.setTitleCache(string);

		return result;

	}

	}

		result.setTitleCache(string, true);

		return result;

	}

            //            specimenImportConfigurator.setDoCreateIndividualsAssociations(true);

            ref.setUuid(UUID.fromString("98b0a618-a95b-464e-943a-25aaaef202f6"));//observations

            ref.setTitle("Chenopodium vulvaria observations from the British Isles");

            //

            specimenImportConfigurator.setReUseTaxon(true);

            reference.setTitleCache("Chenopodium vulvaria observations from the Botanical Society of the British Isles", true);

            Person p = Person.NewInstance();

            p.setFirstname("Quentin");

  static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();

//    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_piB("piB_nephrolepis");

//    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_piB("guianas");

    static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

    private enum FilterType{MODS, TAXON};

    public static void main(String[] args) {

    	String[] spiderModsList = new String[] {"zt03768p138","zt03750p196","zt03666p193","zt03664p068","zt03646p592","zt03507p056","zt03415p057","zt03383p038","zt03305p052","zt03228p068","zt03131p034","zt02963p068","zt02883p068","zt02814p018","zt02739p050","zt02730p043","zt02637p054","zt02593p127","zt02551p068","zt02534p036","zt02526p053","zt02427p035","zt02361p012","zt02267p068","zt02223p047","zt01826p058","zt01775p024","zt01744p040","zt01529p060","zt01004p028","zt00904","zt00872","zt00619","zt00109","DippenaarSchoeman1989Penestominae","Simon1902Cribellates","Simon1903Penestominae","Lehtinen1967CribellatePenestominae"};

    	String[] taxonList = new String[]  {"Campylopus"}; //{"Eupolybothrus","Polybothrus"}, Chenopodium, Lactarius, Campylopus, Nephrolepis, Comaroma (spiders)

//       /*ants Anochetus*/ String[] modsList = new String[] {"3924" /*, "3743", "4375", "6757", "6752", "3481", "21401_fisher_smith_plos_2008", "2592", "4096", "6877", "6192", "8071"  */};

//        String[] modsList = new String[] {"21367", "21365", "8171", "6877", "21820", "3641", "6757"};

//        suite: , };//,"3540555099"};

//        modsList = new String[] {"Zapparoli-1986-Eupolybothrus-fasciatus"};

//    	taxonList = spiderModsList;

    	FilterType filterType = FilterType.TAXON;

    	NomenclaturalCode tnomenclature = NomenclaturalCode.ICNAFP;

        String defaultClassification= null;// "Nephrolepis";

        boolean alwaysUseDefaultClassification = false;

        boolean useOldUnparsedSynonymExtraction = false;

        Map<String,List<URI>>documentMap = new HashMap<String, List<URI>>();

        /*HOW TO HANDLE SECUNDUM REFERENCE*/

        boolean reuseSecundum = askIfReuseSecundum();

        if (!reuseSecundum) {

            secundum = askForSecundum();

        }

        ICdmDataSource destination = cdmDestination;

        TaxonXImportConfigurator config = prepareTaxonXImport(destination,reuseSecundum, secundum, tnomenclature, alwaysUseDefaultClassification);

        config.setUseOldUnparsedSynonymExtraction(useOldUnparsedSynonymExtraction);

        config.setImportClassificationName(defaultClassification);

        log.info("Start import from  TaxonX Data");

     *

     */

    private static void prepareReferenceAndSource(TaxonXImportConfigurator taxonxImportConfigurator, URI source) {

        //            String tref = askQuestion("Import source? (ie Plazi document ID)");

        String tref="PLAZI - "+source.getPath().split("/")[source.getPath().split("/").length-1];

        reference.setTitleCache(tref,true);

        reference.setTitle(tref);

        taxonxImportConfigurator.setSourceReference(reference);

        TaxonXImportConfigurator.setSourceRef(reference);

        referenceUrl.setTitleCache(source.toString(), true);

        referenceUrl.setTitle(source.toString());

        reference.setUri(source);

     * @param destination

     * @param reuseSecundum

     * @param secundum

     * @return

     */

        TaxonXImportConfigurator taxonxImportConfigurator = TaxonXImportConfigurator.NewInstance(destination);

        //taxonxImportConfigurator.setClassificationName(taxonxImportConfigurator.getSourceReferenceTitle());

	}

	private static Map<String, List<String>> fillDocumentMap(FilterType filterType,

					throws MalformedURLException, IOException {

		Map<String, List<String>> documents = new HashMap<String, List<String>>();

		List<String> docList;

		String inputLine;

		            String taxon = inputLine.split("taxon=\"")[1].split("\"")[0];

		            String docID=inputLine.split("docId=\"")[1].split("\"")[0];

		            System.out.println("docID: "+docID);

		            String link=inputLine.split("link=\"")[1].split("\"")[0];

		            String pageStart = inputLine.split("startPage=\"")[1].split("\"")[0];

		            String pageEnd = inputLine.split("endPage=\"")[1].split("\"")[0];

		    }

		}

		System.out.println("documents created");

		return documents;

	}

    /**

     * @return

     */

        //        logger.info("getFullReference for "+ name);

        JTextArea textArea = new JTextArea("Enter the secundum name");

        JScrollPane scrollPane = new JScrollPane(textArea);

                null,

                null,

                null);

        ref.setTitle(s);

        return ref;

    }

		System.out.println("End import from ("+ source.toString() + ")...");

	}

		result.setTitleCache(string, true);

		return result;

	}

/**

 * Copyright (C) 2007 EDIT

 * 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.

 */

import java.util.ListIterator;

import org.apache.log4j.Logger;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.api.application.CdmApplicationController;

	protected ArrayList<String> identificationList = new ArrayList<String>();

	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;

	static ICdmDataSource desitination = CdmDestinations.localH2();

	public void saveUnit(HashMap<String,String> unit){

		String author = unit.get("author");

		TransactionStatus tx = null;

		app = CdmApplicationController.NewInstance(desitination, hbm2dll);

		tx = app.startTransaction();

		try {

			sec.setTitleCache("SYNTHESYS CACHE DATA", true);

			/**

			//create specimen

			if (this.recordBasis != null){

				if (this.recordBasis.toLowerCase().startsWith("s")) {//specimen

				}

				else if (this.recordBasis.toLowerCase().startsWith("o")) {//observation

				}

				else if (this.recordBasis.toLowerCase().startsWith("l")) {//living -> fossil, herbarium sheet....???

				}

			}

			if (derivedThing == null){

				if (this.fullScientificNameString.indexOf("_preferred_") != -1){

					scientificName = this.fullScientificNameString.split("_preferred_")[0];

					String pTmp = this.fullScientificNameString.split("_preferred_")[1];

//				taxonName = nvnpi.parseFullName(this.fullScientificNameString,NomenclaturalCode.ICZN(),null);

//				if (taxonName.hasProblem()){

//				System.out.println("pb ICNCP");

//				}

//				}

//				}

				taxonName = nvnpi.parseFullName(scientificName);

				if (withCdm){

					}

				}

//				tx = app.startTransaction();

				app.getNameService().saveOrUpdate(taxonName);

				taxon = Taxon.NewInstance(taxonName, sec); //TODO use real reference for sec

				System.out.println("Institution (agent) unknown");

				//create institution

				institution = Institution.NewInstance();

			}

			else{

				System.out.println("Institution (agent) already in the db");

				for (int i=0; i<collections.size(); i++){

					collection = collections.get(i);

					try {

							//found a collection with the same code and the same institution

							collectionFound=true;

						}

			gatheringEvent.setExactLocation(coordinates);

			NamedArea area = NamedArea.NewInstance();

			Country country = null;

//			System.out.println("isocountry "+this.isocountry);

//			System.out.println(country.getLabel());

//			Set<Continent> cont = country.getContinents();

//			System.out.println(cont.size());

//			Iterator<Continent> iter = cont.iterator();

//			while (iter.hasNext())

//				System.out.println(iter.next().toString());

			if (country != null){

				area.addCountry(country);

				System.out.println("country not null!");

			/**

			 * SAVE AND STORE DATA

			//save the specimen data

			//	app.getOccurrenceService().saveSpecimenOrObservationBase(fieldObservation);

			try {

			e.printStackTrace();

			result = false;

		}

		app.commitTransaction(tx);

		System.out.println("commit done");

		app.close();

		return result;

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) throws URISyntaxException {

		logger.info("main method");

		SynthesysCacheActivator abcdAct = new SynthesysCacheActivator();

		ArrayList<HashMap<String, String>> units;

		try {

			units = ExcelUtils.parseXLS(uri);

			logger.info(unit);

			abcdAct.saveUnit(unit);//and then invoke

			abcdAct.invoke();

		}

	}

/**

* Copyright (C) 2007 EDIT

* 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.

*/

 */

public class TcsRdfTestActivator {

	private static final Logger logger = Logger.getLogger(TcsRdfTestActivator.class);

	//database validation status (create, update, validate ...)

	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;

	static final String tcsSource = TcsSources.tcsRdf_test();

	static final UUID treeUuid = UUID.fromString("00000000-0c97-48ac-8d33-6099ed68345");

	static final String sourceSecId = "XXX";

	//check - import

	static final CHECK check = CHECK.CHECK_AND_IMPORT;

	//authors

	static final boolean doMetaData = true;

	//references

	//names

	static final boolean doTaxonNames = true;

	static final boolean doRelNames = true;

	//taxa

	static final boolean doTaxa = true;

	static final boolean doRelTaxa = true;

	private void doImport(){

		System.out.println("Start import from Tcs("+ tcsSource.toString() + ") ...");

		//make BerlinModel Source

		URI source;

		try {

			source = new URI(tcsSource);

			ICdmDataSource destination = cdmDestination;

			TcsRdfImportConfigurator tcsImportConfigurator = TcsRdfImportConfigurator.NewInstance(source,  destination);

			tcsImportConfigurator.setClassificationUuid(treeUuid);

			tcsImportConfigurator.setSourceSecId(sourceSecId);

			tcsImportConfigurator.setDoReferences(doReferences);

			tcsImportConfigurator.setDoTaxonNames(doTaxonNames);

			tcsImportConfigurator.setDoRelNames(doRelNames);

			tcsImportConfigurator.setDoTaxa(doTaxa);

			tcsImportConfigurator.setDoRelTaxa(doRelTaxa);

			tcsImportConfigurator.setCheck(check);

			tcsImportConfigurator.setDbSchemaValidation(hbm2dll);

			// invoke import

			CdmDefaultImport<TcsRdfImportConfigurator> tcsImport = new CdmDefaultImport<TcsRdfImportConfigurator>();

			tcsImport.invoke(tcsImportConfigurator);

			IReferenceService refService = tcsImport.getCdmAppController().getReferenceService();

			IBook book = ReferenceFactory.newBook();

			//book.setDatePublished(TimePeriod.NewInstance(1945));

			book.setDatePublished(TimePeriod.NewInstance(1945).setEndDay(12).setEndMonth(4));

			logger.info("End");

			System.out.println("End import from TCS ("+ source.toString() + ")...");

		} catch (URISyntaxException e) {

			e.printStackTrace();

		}

	}

	/**

		TcsRdfTestActivator me = new TcsRdfTestActivator();

		me.doImport();

	}

}

/**

* Copyright (C) 2008 EDIT

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

*/

import eu.etaxonomy.cdm.model.description.TaxonDescription;

import eu.etaxonomy.cdm.model.description.TaxonInteraction;

import eu.etaxonomy.cdm.model.description.TaxonNameDescription;

import eu.etaxonomy.cdm.model.location.Country;

import eu.etaxonomy.cdm.model.name.BotanicalName;

import eu.etaxonomy.cdm.model.name.NomenclaturalCode;

import eu.etaxonomy.cdm.model.name.Rank;

	private static final Logger logger = Logger.getLogger(TestDatabase.class);

	public static ICdmDataSource CDM_DB(String dbname) {

		logger.info("Setting DB " + dbname);

		String password = AccountStore.readOrStorePassword(dbname, server, username, null);

		ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, dbname, username, password, NomenclaturalCode.ICNAFP);

		return datasource;

	}

    public static CdmApplicationController initDb(ICdmDataSource db, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading) {

		logger.info("Initializing database '" + db.getName() + "'");

		CdmApplicationController appCtrInit = CdmIoApplicationController.NewInstance(db, dbSchemaValidation, omitTermLoading);

		return appCtrInit;

    }

	public static void loadTestData(String dbname, CdmApplicationController appCtr) {

		logger.info("Loading test data into " + dbname);

		TransactionStatus txStatus = appCtr.startTransaction();

		DataSet dataSet = buildDataSet();

		appCtr.getTermService().save(dataSet.getTerms());

		appCtr.getTaxonService().save((List)dataSet.getTaxonBases());

		appCtr.commitTransaction(txStatus);

		appCtr.close();

    }

	/**

	 * This method constructs a small sample classification to test JAXB marshaling.

	 * The sample tree contains four taxa. The root taxon has two children taxa, and

		List<AgentBase> agents = new ArrayList<AgentBase>();

	    List<VersionableEntity> agentData = new ArrayList<VersionableEntity>();

	    //List<Agent> agentData = new ArrayList<Agent>();

	    //List<TermBase> terms = new ArrayList<TermBase>();

	    List<DefinedTermBase> terms = new ArrayList<DefinedTermBase>();

	    List<Reference> references = new ArrayList<Reference>();

	    List<TaxonNameBase> taxonomicNames = new ArrayList<TaxonNameBase>();

	    List<TaxonBase> taxonBases = new ArrayList<TaxonBase>();

	    List<Feature> features = new ArrayList<Feature>();

	    Feature feature1 = Feature.BIOLOGY_ECOLOGY();

	    TaxonNameDescription taxNameDescription = TaxonNameDescription.NewInstance();

//	    taxNameDescription.addFeature(feature1);    //no longer supported since v3.3

	    QuantitativeData element = QuantitativeData.NewInstance();

	    statisticalValue.setValue((float) 2.1);

	    element.addStatisticalValue(statisticalValue);

	    taxNameDescription.addElement(element);

	    SpecimenOrObservationBase<?> specimen = DerivedUnit.NewPreservedSpecimenInstance();

	    specimen.setIndividualCount(12);

	    Feature featureIndAss = Feature.INDIVIDUALS_ASSOCIATION();

	    TaxonNameDescription newTaxNameDesc = TaxonNameDescription.NewInstance();

//	    newTaxNameDesc.addFeature(featureIndAss);   //no longer supported since v3.3

	    IndividualsAssociation indAss = IndividualsAssociation.NewInstance();

	    indAss.setAssociatedSpecimenOrObservation(specimen);

	    newTaxNameDesc.addElement(indAss);

//	    List<Synonym> synonyms = new ArrayList<Synonym>();

	    List<AnnotatableEntity> homotypicalGroups;

		BotanicalName name1, name2, name21, nameRoot1, nameFree, synName11, synName12, synName2, synNameFree;

		BotanicalName nameRoot2, nameR2_1, nameR2_2;

		Taxon child1, child2, child21, root1T, root2T, freeT;

		Synonym syn11, syn12, syn2, synFree;

		Rank rankSpecies, rankSubspecies, rankGenus;

		Person linne = new Person("Carl", "Linne", "L.");

		linne.setTitleCache("Linne & Karl", true);

		//Contact contact1 = new Contact();

		//contact1.setEmail("someone@somewhere.org");

		= new InstitutionalMembership(institute, linne, period, "Biodiversity", "Head");

		//agentData.add(contact1);

		rankSpecies = Rank.SPECIES();

		rankSubspecies = Rank.SUBSPECIES();

		rankGenus = Rank.GENUS();

//		terms.add(keyword);

        // taxonomic names

		nameRoot1 = BotanicalName.NewInstance(rankGenus,"Calendula",null,null,null,linne,null,"p.100", null);

		nameRoot1.addDescription(taxNameDescription);

		nameRoot1.addDescription(newTaxNameDesc);

		name1 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"arvensis",null,linne,null,"p.1", null);

		synName11 = BotanicalName.NewInstance(rankSpecies,"Caltha",null,"arvensis",null,linne,null,"p.11", null);

		synName12 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"sancta",null,linne,null,"p.12", null);

		name2 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzae",null,linne,null,"p.2", null);

		synName2 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"echinata",null,linne,null,"p.2", null);

		name21 = BotanicalName.NewInstance(rankSubspecies,"Calendula",null,"lanzea","something",linne,null,"p.1", null);

		//name211 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null);

		//name212 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null);

			BotanicalName.NewInstance(rankGenus,"Sonchus",null,null,null,linne,null,"p.200", null);

		nameR2_1 = BotanicalName.NewInstance(rankSpecies,"Sonchus",null,"child1",null,linne,null,"p.1", null);

		nameR2_2 = BotanicalName.NewInstance(rankSpecies,"Sonchus",null,"child2",null,linne,null,"p.2", null);

		nameFree = BotanicalName.NewInstance(rankSpecies,"Cichorium",null,"intybus",null,linne,null,"p.200", null);

		synNameFree = BotanicalName.NewInstance(rankSpecies,"Cichorium",null,"balearicum",null,linne,null,"p.2", null);

		taxonomicNames.add(nameFree);

		taxonomicNames.add(synNameFree);

		taxonomicNames.add(nameRoot2);

        // references

		sec = ReferenceFactory.newBook();

		sec.setAuthorship(linne);

		sec.setTitleCache("Plant Specification & Taxonomy", true);

		references.add(sec);

		citRef = ReferenceFactory.newDatabase();

		citRef.setAuthorship(linne);

		citRef.setTitleCache("BioCASE", true);

		references.add(citRef);

		// taxa

		root1T = Taxon.NewInstance(nameRoot1, sec);

		root2T = Taxon.NewInstance(nameRoot2, sec);

		freeT = Taxon.NewInstance(nameFree, sec);

		child21 = Taxon.NewInstance(name21, sec);

		childR2_1 = Taxon.NewInstance(nameR2_1, sec);

		childR2_2 = Taxon.NewInstance(nameR2_2, sec);

		//TaxonInteractions

		TaxonInteraction descBase = TaxonInteraction.NewInstance();

		descBase.setTaxon2(root1T);

		Feature hostplant = Feature.HOSTPLANT();

		descBase.setFeature(hostplant);

		TaxonDescription taxDesc = TaxonDescription.NewInstance();

		taxDesc.addElement(descBase);

		root2T.addDescription(taxDesc);

		//locations

		taxDesc = TaxonDescription.NewInstance();

		Feature locationFeature = Feature.DISTRIBUTION();

		//locationFeature.

		Country area = Country.NewInstance("", "locationTest", null);

		area.setType(NamedAreaType.NATURAL_AREA());

		//Country woC= Country.NewInstance();

		area.addCountry(Country.AFGHANISTAN());

		taxDesc.addGeoScope(area);

//		taxDesc.addFeature(locationFeature);   //no longer supported since v3.3

		root1T.addDescription(taxDesc);

		// synonyms

		synFree = Synonym.NewInstance(synNameFree, sec);

		syn11 = Synonym.NewInstance(synName11, sec);

		syn12 = Synonym.NewInstance(synName12, sec);

		syn2 = Synonym.NewInstance(synName2, sec);

		child1.addSynonym(syn11, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF());

		child1.addSynonym(syn12, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());

		child2.addSynonym(syn2, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());

		taxonBases.add(syn11);

		taxonBases.add(syn12);

		taxonBases.add(syn2);

		// taxonomic children

		//TODO: Adapt to classification

		taxTree = Classification.NewInstance("TestTree");

		root1TNode = taxTree.addChildTaxon(root1T, sec, null);

		child1Node = root1TNode.addChildTaxon(child1, null, null);

		child2Node = root1TNode.addChildTaxon(child2, null, null);

		child21Node = child2Node.addChildTaxon(child21, null, null);

		taxTree2 = Classification.NewInstance("TestTree2");

		root2TNode = taxTree2.addChildTaxon(root2T, sec, null);

		root2TNode.addChildTaxon(child1, sec, "p.1010").setSynonymToBeUsed(syn11);

		root2TNode.addChildTaxon(child2, null, null);

		/*

		root1T.addTaxonomicChild(child1, sec, "p.1010");

		root1T.addTaxonomicChild(child2, sec, "p.1020");

		child2.addTaxonomicChild(child21, sec, "p.2000");

		root2T.addTaxonomicChild(child1, sec, "p.1010");

		root2T.addTaxonomicChild(child2, sec, "p.1020");

		*/

		//

		taxonBases.add(root1T);

		taxonBases.add(root2T);

		taxonBases.add(freeT);

		taxonBases.add(child21);

		taxonBases.add(childR2_1);

		taxonBases.add(childR2_2);

		DataSet dataSet = new DataSet();

		logger.warn("WARNING: TestDatabase has been commented in parts. Mainly, must be adapted to classification.");

		dataSet.setTerms(terms);

		dataSet.setAgents(agents);

//		dataSet.setAgentData(agentData); //TODO

		dataSet.setReferences(references);

		dataSet.setTaxonomicNames(taxonomicNames);

		dataSet.setTaxonBases((List)taxonBases);

		return dataSet;

	}

/**

* Copyright (C) 2008 EDIT

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

*/

 * @created 27.10.2008

 */

public class TestTransaction {

	private static final String dbName = "cdm_test_jaxb";

    private static final int MAX_ENTRIES = 20;

	private static final ICdmDataSource db = TestDatabase.CDM_DB(dbName);

    private static final Logger logger = Logger.getLogger(TestTransaction.class);