EDIT

  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;

    }