EDIT

package eu.etaxonomy.taxeditor.view.dataimport.e4;

import java.time.LocalDate;

import java.time.format.DateTimeFormatter;

import java.util.ArrayList;

import java.util.Collection;

import java.util.Collections;

import java.util.Comparator;

import java.util.HashSet;

import java.util.List;

import java.util.Set;

import org.eclipse.core.runtime.jobs.Job;

import org.eclipse.jface.action.Action;

import org.eclipse.swt.widgets.Table;

import org.eclipse.swt.widgets.TableItem;

import eu.etaxonomy.cdm.common.URI;

import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;

import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseResponse;

import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifDataSetProtocol;

import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse;

import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;

import eu.etaxonomy.cdm.io.specimen.gbif.in.GbifImportConfigurator;

import eu.etaxonomy.taxeditor.preference.PreferencesUtil;

import eu.etaxonomy.taxeditor.store.CdmStore;

import eu.etaxonomy.taxeditor.view.dataimport.GbifResponseComparator;

/**

 * @author pplitzner

 * @since Oct 4, 2017

 */

public class SaveImportedSpecimenAction extends Action {

    private Comparator<GbifResponse> comparator;

    private DataImportView<?> dataImportView;

    public SaveImportedSpecimenAction(DataImportView<?> dataImportView) {

        super();

        this.dataImportView = dataImportView;

    }

    @Override

    public void run() {

        Table table = dataImportView.getTable();

        Collection<GbifResponse> checkedResults = new HashSet<>();

        Collection<BioCaseResponse> checkedAbcdResults = new HashSet<>();

        Object data;

        Set<String[]> unitIdsGbif = new HashSet<>();

        Set<String[]> unitIdsBioCase = new HashSet<>();

        List<GbifResponse> biocaseResponses = new ArrayList<>();

        for(TableItem item:table.getItems()){

            if(item.getChecked()){

                //Save Specimen

                data = item.getData();

                if(data instanceof GbifResponse){

                    checkedResults.add((GbifResponse)item.getData());

                }

                if(data instanceof BioCaseResponse){

                    checkedAbcdResults.add((BioCaseResponse)data);

                }

            }

        }

        String[] tripleId ;

        for (GbifResponse response:checkedResults){

            if (response != null){

                tripleId = response.getTripleID();

                if (response.getDataSetProtocol()!=null && response.getDataSetProtocol().equals(GbifDataSetProtocol.BIOCASE)){

                    biocaseResponses.add(response);

                }else{

                    unitIdsGbif.add(tripleId);

                }

            }

        }

        Collections.sort(biocaseResponses, getComparator());

        Abcd206ImportConfigurator configuratorAbcd;

        List<Abcd206ImportConfigurator> abcdConfigurators = new ArrayList<>();

        OccurenceQuery bioCaseOccurrenceQuery = null;

        URI dataSetUri = null;

        for (BioCaseResponse response:checkedAbcdResults){

            if (!response.getDataSetUri().equals(dataSetUri)){

                dataSetUri = response.getDataSetUri();

                //configuratorAbcd = Abcd206ImportConfigurator.NewInstance(null, null);

                configuratorAbcd = PreferencesUtil.getLastUsedAbcdImportConfigurator();

                if (configuratorAbcd != null){

                    if (configuratorAbcd.getNomenclaturalCode() == null){

                        configuratorAbcd.setNomenclaturalCode(PreferencesUtil.getPreferredNomenclaturalCode());

                    }

                }else{

                    configuratorAbcd = Abcd206ImportConfigurator.NewInstance(null, null);

                    if (configuratorAbcd.getNomenclaturalCode() == null){

                        configuratorAbcd.setNomenclaturalCode(PreferencesUtil.getPreferredNomenclaturalCode());

                    }

                }

                configuratorAbcd.setSourceUri(dataSetUri);

                if (configuratorAbcd.getSourceReference() == null && configuratorAbcd.getSourceRefUuid() == null){

                    DateTimeFormatter dtf = DateTimeFormatter.ofPattern("yyyy/MM/dd");

                    LocalDate localDate = LocalDate.now();

                    String sourceRef ="Specimen Import " + localDate.toString();

                    configuratorAbcd.setSourceReferenceTitle(sourceRef);

                }

                unitIdsBioCase = new HashSet<>();

                bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);

                configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);

//                if (dataImportView.getClassification() != null){

//                    configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());

//                }

//                if (dataImportView.getReferenceString() != null){

//                    configuratorAbcd.setSourceReferenceTitle(dataImportView.getReferenceString());

//                }

                abcdConfigurators.add(configuratorAbcd);

            }

            tripleId = response.getTripleID();

            unitIdsBioCase.add(tripleId);

        }

        //                if (!unitIdsBioCase.isEmpty()){

        //                    configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false);

        //                    configuratorAbcd.addMediaAsMediaSpecimen(true);

        //                    configuratorAbcd.setIgnoreAuthorship(true);

        //                    configuratorAbcd.setMoveNewTaxaToDefaultClassification(false);

        //                    if (configuratorAbcd != null){

        //                        abcdConfigurators.add(configuratorAbcd);

        //                    }

        ////                    unitIdsBioCase = new HashSet<String[]>();

        //                    bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);

        //                    configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);

        //                    configuratorAbcd.setGetSiblings(true);

        //                    if (dataImportView.getClassification() != null){

        //                        configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());

        //                    }

        //                }

        //                for (GbifResponse response: biocaseResponses){

        //                	try {

        //						dataSetResponse = new GbifQueryServiceWrapper().queryOriginalDataSet(response);

        //						dataSetUri = dataSetResponse.getEndpoint();

        //					} catch (ClientProtocolException e) {

        //						// TODO Auto-generated catch block

        //						e.printStackTrace();

        //					} catch (IOException e) {

        //						// TODO Auto-generated catch block

        //						e.printStackTrace();

        //					}

        //                	if (!response.getDataSetUri().equals(dataSetUri)){

        //                		configuratorAbcd = Abcd206ImportConfigurator.NewInstance(dataSetUri, null, false);

        //                		configuratorAbcd.addMediaAsMediaSpecimen(true);

        //                		configuratorAbcd.setIgnoreAuthorship(true);

        //                		configuratorAbcd.setMoveNewTaxaToDefaultClassification(false);

        //                		if (configuratorAbcd != null){

        //                			abcdConfigurators.add(configuratorAbcd);

        //                		}

        //                		unitIdsBioCase = new HashSet<String[]>();

        //                		bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);

        //                		configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);

        //                		configuratorAbcd.setGetSiblings(true);

        //                		if (dataImportView.getClassification() != null){

        //                			configuratorAbcd.setClassificationUuid(dataImportView.getClassification().getUuid());

        //                		}

        //

        //                	}

        //                	tripleId = response.getTripleID();

        //                	unitIdsBioCase.add(tripleId);

        //                }

        //  configurator.setQuery(query);

        if (!checkedAbcdResults.isEmpty()){

            Job bioCaseJob = CdmStore.getImportManager().createIOServiceJob(abcdConfigurators);

            CdmStore.getImportManager().run(bioCaseJob);

        }

        if (!unitIdsGbif.isEmpty()){

            OccurenceQuery query = new OccurenceQuery(unitIdsGbif);

            GbifImportConfigurator configurator = GbifImportConfigurator.newInstance(query);

            configurator.setSourceReferenceTitle("Import Gbif data");

            Job gbifJob = CdmStore.getImportManager().createIOServiceJob(configurator);

            CdmStore.getImportManager().run(gbifJob);

        }

    }

    @Override

    public String getText() {

        return "Import";

    }

    private Comparator<GbifResponse> getComparator(){

        if (comparator == null){

            comparator = new GbifResponseComparator();

        }

        return comparator;

    }

}