EDIT

/**

* Copyright (C) 2014 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.taxeditor.view.dataimport.e4;

import java.io.IOException;

import java.io.InputStream;

import java.net.URI;

import java.util.ArrayList;

import java.util.Collection;

import org.apache.http.client.ClientProtocolException;

import org.w3c.dom.Element;

import org.w3c.dom.NodeList;

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

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

import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206DataHolder;

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

import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportParser;

import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportState;

import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206XMLFieldGetter;

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

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

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

import eu.etaxonomy.taxeditor.model.MessagingUtils;

/**

 * @author pplitzner

 * @date Sep 3, 2014

 */

public class SpecimenImportViewE4 extends DataImportViewE4<BioCaseResponse> {

    public static final String ID = "eu.etaxonomy.taxeditor.view.dataimport.SpecimenImportView"; //$NON-NLS-1$

    private URI endPoint;

    public SpecimenImportViewE4() {

    }

    public void setEndpoint(URI endPoint) {

        this.endPoint = endPoint;

    }

    @Override

    protected String getTextForTableItem(BioCaseResponse item) {

        //TODO: could be defined in user preferences...

        String name = null;

        if(!(((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList() == null) && !((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList().isEmpty()){

           Identification identification =  ((Abcd206DataHolder)item.getAbcdDataHolder()).getIdentificationList().iterator().next();

           name = identification.getScientificName();

        }

        if (name != null){

            return name +" - "+((Abcd206DataHolder)item.getAbcdDataHolder()).getCollectionCode() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getUnitID() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getKindOfUnit();

        }else {

            return ((Abcd206DataHolder)item.getAbcdDataHolder()).getCollectionCode() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getUnitID() + " - "+ ((Abcd206DataHolder)item.getAbcdDataHolder()).getKindOfUnit();

        }

    }

    @Override

    public void query() {

        String errorMessage = "Could not execute query " + query;

        Collection<BioCaseResponse> results = new ArrayList<BioCaseResponse>();

        try {

            //FIXME move ABCD import to cdmlib -> this will also get rid of the transient services

            InputStream resultStream;

            resultStream = new BioCaseQueryServiceWrapper().query(query, endPoint);

            Abcd206ImportConfigurator configurator = Abcd206ImportConfigurator.NewInstance(null, null);

            configurator.setSourceUri(endPoint);

            //            TransientCdmRepository repo =

//                    new TransientCdmRepository(CdmStore.getCurrentApplicationConfiguration());

            //configurator.setCdmAppController(repo);

            //TODO: do not query all data but with the selected triple IDs -> see GbifResponseImportView

            configurator.setAddMediaAsMediaSpecimen(true);

            configurator.setAllowReuseOtherClassifications(true);

            configurator.setMoveNewTaxaToDefaultClassification(false);

            UnitAssociationWrapper unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(resultStream, null);

            NodeList unitsList = unitAssociationWrapper.getAssociatedUnits();

            Abcd206DataHolder dataHolder = new Abcd206DataHolder();

            Abcd206XMLFieldGetter abcdFieldGetter = new Abcd206XMLFieldGetter(dataHolder, unitAssociationWrapper.getPrefix());

            Abcd206ImportState state = new Abcd206ImportState(configurator);

            state.setDataHolder(dataHolder);

            BioCaseResponse response = null;

            if (unitsList != null){

                for (int i = 0; i <unitsList.getLength(); i++){

                    Element item = (Element) unitsList.item(i);

                    dataHolder = new Abcd206DataHolder();

                    abcdFieldGetter = new Abcd206XMLFieldGetter(dataHolder, unitAssociationWrapper.getPrefix());

                    state.setPrefix(unitAssociationWrapper.getPrefix());

                    Abcd206ImportParser.setUnitPropertiesXML(item, abcdFieldGetter, state);

                    String[] tripleIdBioCase = new String[3];

                    tripleIdBioCase[0] =dataHolder.getUnitID();

                    tripleIdBioCase[1] = dataHolder.getInstitutionCode();

                    tripleIdBioCase[2] = dataHolder.getCollectionCode();

                    response = new BioCaseResponse(dataHolder, endPoint, tripleIdBioCase );

                    results.add(response);

                }

            }

//            Job job = CdmStore.getImportManager().createIOServiceJob(configurator, resultStream, SOURCE_TYPE.INPUTSTREAM);

//            CdmStore.getImportManager().run(job);

            setResults(results);

        } catch (ClientProtocolException e) {

            MessagingUtils.error(getClass(), e);

           // logger.error(errorMessage, e);

        } catch (IOException e) {

            //logger.error(errorMessage, e);

            MessagingUtils.error(getClass(), e);

        }

       // setResults(results);

    }

}