EDIT

package eu.etaxonomy.taxeditor.view.dataimport;

import java.io.IOException;

import java.net.URI;

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.apache.http.client.ClientProtocolException;

import org.apache.log4j.Logger;

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

import org.eclipse.jface.action.Action;

import org.eclipse.jface.text.source.Annotation;

import org.eclipse.swt.widgets.Table;

import org.eclipse.swt.widgets.TableItem;

import org.eclipse.ui.IWorkbenchPart;

import org.eclipse.ui.IWorkbenchWindow;

import org.eclipse.ui.PlatformUI;

import eu.etaxonomy.cdm.api.conversation.ConversationHolder;

import eu.etaxonomy.cdm.api.service.IOccurrenceService;

import eu.etaxonomy.cdm.api.service.ITermService;

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

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

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

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

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.*;

import eu.etaxonomy.cdm.model.common.DefinedTermBase;

import eu.etaxonomy.cdm.model.common.ICdmBase;

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

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

import eu.etaxonomy.taxeditor.store.CdmStore;

public class SaveImportedSpecimenAction extends Action {

    private final Logger logger = Logger.getLogger(SaveImportedSpecimenAction.class);

    private Comparator<GbifResponse> comparator;

    /* (non-Javadoc)

     * @see org.eclipse.jface.action.Action#run()

     */

    @Override

    public void run() {

        final IWorkbenchWindow window = PlatformUI.getWorkbench().getActiveWorkbenchWindow();

        IWorkbenchPart activePart = window.getActivePage().getActivePart();

        if(activePart instanceof DataImportView<?>){

            DataImportView<?> dataImportView = (DataImportView<?>)activePart;

            Table table = dataImportView.getTable();

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

            Object data;

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

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

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

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

                if(item.getChecked()){

                    //Save Specimen

                	 data = item.getData();

                	 if(data instanceof GbifResponse){

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

                	 }

                }

            }

            String[] tripleId ;

                for (GbifResponse response:checkedResults){

                	if (response != null){

                		tripleId = response.getTripleID();

                		if (response.getDataSetProtocol().equals(GbifDataSetProtocol.BIOCASE)){

                			biocaseResponses.add(response);

                		}else{

                			unitIdsGbif.add(tripleId);

                		}

                	}

                }

                Collections.sort(biocaseResponses, getComparator()); 

                URI dataSetUri = null;

                Abcd206ImportConfigurator configuratorAbcd;

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

                DataSetResponse dataSetResponse;

                OccurenceQuery bioCaseOccurrenceQuery = null;

                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);

                		if (configuratorAbcd != null){

                			abcdConfigurators.add(configuratorAbcd);

                		}

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

                		bioCaseOccurrenceQuery = new OccurenceQuery(unitIdsBioCase);

                		configuratorAbcd.setOccurenceQuery(bioCaseOccurrenceQuery);

                	}

                	tripleId = response.getTripleID();

                	unitIdsBioCase.add(tripleId);

                }

                OccurenceQuery query = new OccurenceQuery(unitIdsGbif);

                GbifImportConfigurator configurator = GbifImportConfigurator.newInstance(query);

                configurator.setSourceReferenceTitle("Import Gbif data");

                //  configurator.setQuery(query);

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

               CdmStore.getImportManager().run(bioCaseJob);

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

               CdmStore.getImportManager().run(gbifJob);

            }

        }

    private void persistTerm(DefinedTermBase<?> term, ITermService termService, ConversationHolder conversation){

        if(term!=null){

            //if the term does not exist in the DB save it

            if(termService.find(term.getUuid())==null){

                termService.saveOrUpdate(term);

            }

        }

    }

    /* (non-Javadoc)

     * @see org.eclipse.jface.action.Action#getText()

     */

    @Override

    public String getText() {

        return "Import";

    }

    private Comparator<GbifResponse> getComparator(){

    	if (comparator == null){

    		comparator = new GbifResponseComparator();

    	}

    	return comparator;

    }

}