EDIT

/**

* Copyright (C) 2007 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.vibrant;

import java.lang.reflect.Method;

import java.sql.ResultSet;

import java.util.UUID;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources;

import eu.etaxonomy.cdm.app.common.CdmDestinations;

import eu.etaxonomy.cdm.database.DatabaseTypeEnum;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;

import eu.etaxonomy.cdm.io.common.CdmDefaultImport;

import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;

import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;

import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;

import eu.etaxonomy.cdm.io.common.Source;

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

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

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

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

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

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

/**

 * TODO add the following to a wiki page:

 * HINT: If you are about to import into a mysql data base running under windows and if you wish to dump and restore the resulting data bas under another operation systen 

 * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.

 * 

 * 

 * @author a.mueller

 *

 */

public class IopiActivator {

	private static final Logger logger = Logger.getLogger(IopiActivator.class);

	//database validation status (create, update, validate ...)

	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;

	static final Source berlinModelSource = BerlinModelSources.iopi();

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

	static final ICdmDataSource cdmDestination = cdm_test_local_iopi();

	static final boolean useSingleClassification = true;

	static final Integer sourceSecId = 1892; //7000000; 

	static final UUID classificationUuid = null; //UUID.fromString("aa3fbaeb-f5dc-4e75-8d60-c8f93beb7ba6");

	static final UUID sourceRefUuid = UUID.fromString("df68c748-3c64-4b96-9a47-db51fb9d387e");

	// set to zero for unlimited nameFacts

	static final int maximumNumberOfNameFacts = 0;

	static final int partitionSize = 1500;

	//check - import

	static final CHECK check = CHECK.CHECK_AND_IMPORT;

	//editor - import

	static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;

	//NomenclaturalCode

	static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;

	//ignore null

	static final boolean ignoreNull = true;

	static boolean useClassification = true;

	//filter

	static String taxonTable = "v_cdm_exp_taxaAll";

	static String classificationQuery = " SELECT DISTINCT t.PTRefFk, r.RefCache FROM PTaxon t INNER JOIN Reference r ON t.PTRefFk = r.RefId WHERE t.PTRefFk = " + sourceSecId; 

	static String relPTaxonIdQuery = " SELECT r.RelPTaxonId " + 

					" FROM RelPTaxon AS r INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk ";

	static String nameIdTable = " v_cdm_exp_namesAll ";

	static String referenceIdTable = " v_cdm_exp_refAll ";

	static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll )";

	static String authorTeamFilter = null; // " authorTeamId IN (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) ";

	static String authorFilter = null;  // " authorId IN (SELECT authorId FROM v_cdm_exp_authorsAll) "; 

	//not used

	static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";

	static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )"; 

	static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";

// **************** ALL *********************	

	//authors

	static final boolean doAuthors = true;

	//references

	static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;

	//names

	static final boolean doTaxonNames = true;

	static final boolean doRelNames = true;

	static final boolean doNameStatus = true;

	//taxa

	static final boolean doTaxa = true;

	static final boolean doRelTaxa = true;

	static final boolean doFacts = true;

	//etc.

// **************** SELECTED *********************

//	static final boolean doUser = true;

//	//authors

//	static final boolean doAuthors = false;

//	//references

//	static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;

//	//names

//	static final boolean doTaxonNames = false;

//	static final boolean doRelNames = false;

//	static final boolean doNameStatus = false;

//	static final boolean doTypes = false;

//	static final boolean doNameFacts = false;

//	

//	//taxa 

//	static final boolean doTaxa = false;

//	static final boolean doRelTaxa = false;

//	static final boolean doFacts = false;

//	

//	//etc.

//	static final boolean doMarker = false;

//******** ALWAYS IGNORE *****************************

	static final boolean doUser = false;

	static final boolean doOccurences = false;

	static final boolean doCommonNames = false;

	static final boolean doTypes = false;  

	static final boolean doNameFacts = false;

	static final boolean doMarker = false;

	public void importIopi (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){

		System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");

		//make BerlinModel Source

		BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source,  destination);

		config.setClassificationUuid(classificationUuid);

		config.setSourceSecId(sourceSecId);

		config.setNomenclaturalCode(nomenclaturalCode);

		try {

			Method makeUrlMethod = this.getClass().getDeclaredMethod("makeUrlForTaxon", TaxonBase.class, ResultSet.class);

			config.setMakeUrlForTaxon(makeUrlMethod);

		} catch (Exception e) {

			e.printStackTrace();

			return;

		}

		config.setIgnoreNull(ignoreNull);

		config.setDoAuthors(doAuthors);

		config.setDoReferences(doReferences);

		config.setDoTaxonNames(doTaxonNames);

		config.setDoRelNames(doRelNames);

		config.setDoNameStatus(doNameStatus);

		config.setDoTypes(doTypes);

		config.setDoNameFacts(doNameFacts);

		config.setUseClassification(useClassification);

		config.setSourceRefUuid(sourceRefUuid);

		config.setDoTaxa(doTaxa);

		config.setDoRelTaxa(doRelTaxa);

		config.setDoFacts(doFacts);

		config.setDoOccurrence(doOccurences);

		config.setDoCommonNames(doCommonNames);

		config.setDoMarker(doMarker);

		config.setDoUser(doUser);

		config.setEditor(editor);

		config.setDbSchemaValidation(hbm2dll);

		// maximum number of name facts to import

		config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);

		config.setUseSingleClassification(useSingleClassification);

		config.setCheck(check);

		config.setEditor(editor);

		config.setRecordsPerTransaction(partitionSize);

//		filter

		config.setTaxonTable(taxonTable);

		config.setClassificationQuery(classificationQuery);

		config.setRelTaxaIdQuery(relPTaxonIdQuery);

		config.setNameIdTable(nameIdTable);

		config.setReferenceIdTable(referenceIdTable);

		config.setAuthorTeamFilter(authorTeamFilter);

		config.setAuthorFilter(authorFilter);

		config.setFactFilter(factFilter);

		config.setCommonNameFilter(commonNameFilter);

		config.setOccurrenceFilter(occurrenceFilter);

		config.setOccurrenceSourceFilter(occurrenceSourceFilter);

		config.setUseSingleClassification(useSingleClassification);

		// invoke import

		CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();

		bmImport.invoke(config);

		System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		IopiActivator importActivator = new IopiActivator();

		Source source = berlinModelSource;

		ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;

		importActivator.importIopi(source, cdmRepository, hbm2dll);

	}

	public static ICdmDataSource cdm_test_local_iopi(){

		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;

		String cdmServer = "127.0.0.1";

		String cdmDB = "iopi"; 

		String cdmUserName = "root";

		return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);

	}

	//for FAUNA Europaea (http://rbg-web2.rbge.org.uk/FE/fe.html)

	private static final String URLbase = "http://rbg-web2.rbge.org.uk/cgi-bin/nph-readbtree.pl/feout?FAMILY_XREF=%s&GENUS_XREF=%s&SPECIES_XREF=%s&TAXON_NAME_XREF=%s&RANK=%s";

	public static Method makeUrlForTaxon(TaxonBase<?> taxon, ResultSet rs){

		Method result = null;

		ExtensionType urlExtensionType = ExtensionType.URL();

		String family = "";

		String genus = "";

		String species = "";

		String taxonName = "";

		String rankStr = "";

		NonViralName<?>  name = CdmBase.deproxy(taxon.getName(), NonViralName.class);

		Rank rank = name.getRank();

		rankStr = transformFeRanks(rank);

		if (rank.equals(Rank.FAMILY())){

			family = name.getGenusOrUninomial();

			taxonName = name.getGenusOrUninomial();

		}else if (rank.isHigher(Rank.GENUS())){

			taxonName = name.getGenusOrUninomial();

		}else if (rank.isGenus()){

			genus = name.getGenusOrUninomial();

			rankStr = "genus";

		}else if (rank.isInfraGeneric()){

			genus = name.getGenusOrUninomial();

			taxonName = name.getInfraGenericEpithet();

		}else if (rank.isSpecies()){

			genus = name.getGenusOrUninomial();

			species = name.getSpecificEpithet();

			rankStr = "species";

		}else if (rank.isInfraSpecific()){

			genus = name.getGenusOrUninomial();

			species = name.getSpecificEpithet();

			taxonName = name.getInfraSpecificEpithet();

		}

		String url = String.format(URLbase ,family, genus, species, taxonName, rankStr);

		taxon.addExtension(url, urlExtensionType);

		return result;

	}

	private static String transformFeRanks(Rank rank){

		if (rank.equals(Rank.SPECIESAGGREGATE())){ return "agg.";

		}else if (rank.equals(Rank.CLASS())){ return "Class";

		}else if (rank.equals(Rank.DIVISION())){ return "Division";

		}else if (rank.equals(Rank.FAMILY())){ return "family";

		}else if (rank.equals(Rank.FORM())){ return "forma";

		}else if (rank.equals(Rank.GENUS())){ return "genus";

		}else if (rank.equals(Rank.GREX())){ return "grex";

		}else if (rank.equals(Rank.SPECIESGROUP())){ return "group";

		}else if (rank.equals(Rank.ORDER())){ return "Order";

//		}else if (rank.equals(Rank.PROL())){ return "proles";

//--		}else if (rank.equals(Rank.RACE())){ return "race";

		}else if (rank.equals(Rank.SECTION_BOTANY())){ return "Sect.";

		}else if (rank.equals(Rank.SERIES())){ return "Ser.";

		}else if (rank.equals(Rank.SPECIES())){ return "species";

		}else if (rank.equals(Rank.SUBCLASS())){ return "Subclass";

		}else if (rank.equals(Rank.SUBDIVISION())){ return "Subdivision";

		}else if (rank.equals(Rank.SUBFORM())){ return "Subf.";

		}else if (rank.equals(Rank.SUBGENUS())){ return "Subgen.";

		}else if (rank.equals(Rank.SUBORDER())){ return "Suborder";

		}else if (rank.equals(Rank.SUBSECTION_BOTANY())){ return "Subsect.";

		}else if (rank.equals(Rank.SUBSERIES())){ return "Subser.";

		}else if (rank.equals(Rank.SUBSPECIES())){ return "subsp";

		}else if (rank.equals(Rank.SUBVARIETY())){ return "subvar.";

		}else if (rank.equals(Rank.SUPERORDER())){ return "Superorder";

		}else if (rank.equals(Rank.TRIBE())){ return "Tribe";

		}else if (rank.equals(Rank.VARIETY())){ return "var.";

		}else{

			logger.debug("Rank not found: " + rank.getTitleCache());

			return "";

		}	

	}

}