EDIT

/**

* Copyright (C) 2017 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.cdm.app.eflora;

import java.net.URI;

import java.util.ArrayList;

import java.util.List;

import java.util.UUID;

import org.springframework.transaction.TransactionStatus;

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

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

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.ext.ipni.IpniService;

import eu.etaxonomy.cdm.ext.ipni.IpniServiceNamesConfigurator;

import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper;

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

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

import eu.etaxonomy.cdm.model.reference.Reference;

import eu.etaxonomy.cdm.model.reference.ReferenceFactory;

import eu.etaxonomy.cdm.model.taxon.Classification;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonBase;

/**

 * @author a.mueller

 * @date 27.02.2017

 *

 */

public class NepenthaceIpniActivator {

    static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;

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

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

  static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();

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

  static final URI ipniFile = URI.create("file:////BGBM-PESIHPC/FloraMalesianaXml/advPlantNameSearch.txt");

  private void doImport(ICdmDataSource cdmDestination){

      if (cdmDestination.getDatabaseType().equals(CdmDestinations.localH2().getDatabaseType())){

          hbm2dll = DbSchemaValidation.CREATE;

      }

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

      ICdmRepository repository = null  ; //app  for now we do not want to deduplicate against repository

      ImportDeduplicationHelper<?> deduplicationHelper = new ImportDeduplicationHelper<>(repository);

      TransactionStatus txStatus = app.startTransaction();

      Reference ipniSec = app.getReferenceService().find(UUID.fromString("17ffcbc7-7f80-42cd-a95e-25d0289c9f71"));

      if (ipniSec == null){

          ipniSec = ReferenceFactory.newGeneric();

          ipniSec.setTitle("IPNI");

      }

      IpniServiceNamesConfigurator namesConfig = IpniServiceNamesConfigurator.NewInstance();

      namesConfig.setDoApni(false);

      namesConfig.setDoGci(false);

      Classification classification = Classification.NewInstance("IPNI Nepenthes (IK)");

      classification.setUuid(UUID.fromString("89b1a50a-15f5-415b-9ab8-b98ffb6d3c5a"));

      classification.setReference(ipniSec);

      app.getClassificationService().save(classification);

      doSingleImport(app, ipniSec, classification, namesConfig, deduplicationHelper);

      classification = Classification.NewInstance("IPNI Nepenthes (APNI)");

      classification.setUuid(UUID.fromString("c9d1371a-c77a-4249-8406-bb0cb0c1b6f2"));

      classification.setReference(ipniSec);

      app.getClassificationService().save(classification);

      namesConfig.setDoApni(true);

      namesConfig.setDoIk(false);

      doSingleImport(app, ipniSec, classification, namesConfig, deduplicationHelper);

      classification = Classification.NewInstance("IPNI Nepenthes (GCI)");

      classification.setUuid(UUID.fromString("ecddac67-95d6-49ff-a1f3-83e167d581f5"));

      classification.setReference(ipniSec);

      app.getClassificationService().save(classification);

      namesConfig.setDoApni(false);

      namesConfig.setDoGci(true);

      doSingleImport(app, ipniSec, classification, namesConfig, deduplicationHelper);

      app.commitTransaction(txStatus);

////      CSVReader csvReader = new CSVReader(reader);

//

//      List<String[]> allLines = csvReader.readAll();

//

//      for (String[] nextLine : allLines){

//          handleSingleLine(app, nextLine);

//      }

   }

/**

 * @param app

 * @param ipniSec

 * @param classification

 * @param ipniService

 * @param rank

 * @param namesConfig

 */

private void doSingleImport(CdmApplicationController app, Reference ipniSec, Classification classification,

        IpniServiceNamesConfigurator namesConfig, ImportDeduplicationHelper<?> deduplicationHelper) {

    IpniService ipniService = new IpniService();//(IpniService)app.getBean("ipniService");

    Rank rank = null;

      List<IBotanicalName> names = ipniService.getNamesAdvanced(null, "Nepenthes", null, null, null, null,

              null, null, rank, namesConfig, app);

      System.out.println(names.size());

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

      for (IBotanicalName name : names){

//          System.out.println(name.getTitleCache());

          deduplicationHelper.replaceAuthorNamesAndNomRef(null, name);

          Taxon taxon = Taxon.NewInstance(name, ipniSec);

          classification.addChildTaxon(taxon, null, null);

//          app.getTaxonService().saveOrUpdate(taxon);

          taxaToSave.add(taxon);

      }

      app.getTaxonService().saveOrUpdate(taxaToSave);

      app.getClassificationService().saveOrUpdate(classification);

}

  /**

   * @param args

   */

  public static void main(String[] args) {

      NepenthaceIpniActivator me = new NepenthaceIpniActivator();

      me.doImport(cdmDestination);

      System.exit(0);

  }

}