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.eflora;

import java.net.URI;

import java.util.List;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.transaction.TransactionStatus;

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

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

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

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

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

import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;

import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;

import eu.etaxonomy.cdm.io.eflora.EfloraImportConfigurator;

import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer;

import eu.etaxonomy.cdm.model.description.Feature;

import eu.etaxonomy.cdm.model.description.FeatureNode;

import eu.etaxonomy.cdm.model.description.FeatureTree;

import eu.etaxonomy.cdm.model.description.PolytomousKey;

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

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

/**

 * @author a.mueller

 * @created 20.06.2008

 * @version 1.0

 */

public class FloraMalesianaActivator {

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

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

	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;

	static final URI fmSource1 = EfloraSources.fm_sapindaceae_local();

	static final URI fmSource2 = EfloraSources.fm_sapindaceae2_local();

	static final URI fmSource13_1 = EfloraSources.fm_13_1_local();

	static final URI fmSource13_2 = EfloraSources.fm_13_2_local();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3();

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

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

	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();

	//feature tree uuid

	public static final UUID featureTreeUuid = UUID.fromString("168df0c6-6429-484c-b26f-ded1f7e44bd9");

	//classification

	static final UUID classificationUuid = UUID.fromString("ca4e4bcb-a1d1-4124-a358-a3d3c41dd450");

	//check - import

	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	static boolean doPrintKeys = false;

	//taxa

	static final boolean doTaxa = true;

	private boolean includeSapindaceae1 = true;

	private boolean includeSapindaceae2 = true;

	private boolean includeVol13_1 = false;

	private boolean includeVol13_2 = false;

	private void doImport(ICdmDataSource cdmDestination){

		//make Source

		URI source = fmSource1;

		EfloraImportConfigurator floraMalesianaConfig= EfloraImportConfigurator.NewInstance(source, cdmDestination);

		floraMalesianaConfig.setTaxonomicTreeUuid(classificationUuid);

		floraMalesianaConfig.setDoTaxa(doTaxa);

		floraMalesianaConfig.setCheck(check);

		floraMalesianaConfig.setDoPrintKeys(doPrintKeys);

		floraMalesianaConfig.setDbSchemaValidation(hbm2dll);

		CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>();

		//Sapindaceae1

		if (includeSapindaceae1){

			System.out.println("Start import from ("+ fmSource1.toString() + ") ...");

			floraMalesianaConfig.setSourceReference(getSourceReference("Flora Malesiana - Sapindaceae I"));

			myImport.invoke(floraMalesianaConfig);

			System.out.println("End import from ("+ fmSource1.toString() + ")...");

		}

		//Sapindaceae2

		if (includeSapindaceae2){

			System.out.println("\nStart import from ("+ fmSource2.toString() + ") ...");

			source = fmSource2;

			floraMalesianaConfig.setSource(source);

			floraMalesianaConfig.setSourceReference(getSourceReference("Flora Malesiana - Sapindaceae II"));

			myImport.invoke(floraMalesianaConfig);

			System.out.println("End import from ("+ fmSource2.toString() + ")...");

		}

		floraMalesianaConfig.setSourceReference(getSourceReference("Flora Malesiana - Vol. 13"));

		//Vol13_1

		if (includeVol13_1){

			System.out.println("\nStart import from ("+ fmSource13_1.toString() + ") ...");

			source = fmSource13_1;

			floraMalesianaConfig.setSource(source);

			myImport.invoke(floraMalesianaConfig);

			System.out.println("End import from ("+ fmSource13_1.toString() + ")...");

		}

		//Vol13_2

		if (includeVol13_2){

			System.out.println("\nStart import from ("+ fmSource13_2.toString() + ") ...");

			source = fmSource13_2;

			floraMalesianaConfig.setSource(source);

			myImport.invoke(floraMalesianaConfig);

			System.out.println("End import from ("+ fmSource13_2.toString() + ")...");

		}

		FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());

		myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);

		//check keys

		if (doPrintKeys){

			TransactionStatus tx = myImport.getCdmAppController().startTransaction();

			List<FeatureTree> keys = myImport.getCdmAppController().getFeatureTreeService().list(PolytomousKey.class, null, null, null, null);

			for(FeatureTree key : keys){

				((PolytomousKey)key).print(System.out);

				System.out.println();

			}

			myImport.getCdmAppController().commitTransaction(tx);

		}

	}

	private ReferenceBase getSourceReference(String string) {

		ReferenceBase result = ReferenceFactory.newGeneric();

		result.setTitleCache(string);

		return result;

	}

	private FeatureTree makeFeatureNode(ITermService service){

		FloraMalesianaTransformer transformer = new FloraMalesianaTransformer();

		FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);

		result.setTitleCache("Flora Malesiana Presentation Feature Tree");

		FeatureNode root = result.getRoot();

		FeatureNode newNode;

		newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());

		root.addChild(newNode);

		addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);

		addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service);

		newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());

		root.addChild(newNode);

		newNode = FeatureNode.NewInstance(Feature.ECOLOGY());

		root.addChild(newNode);

		addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);

		newNode = FeatureNode.NewInstance(Feature.USES());

		root.addChild(newNode);

		addFeataureNodesByStringList(chomosomesList, root, transformer, service);

		newNode = FeatureNode.NewInstance(Feature.CITATION());

		root.addChild(newNode);

		return result;

	}

	private static String [] chomosomesList = new String[]{

		"Chromosomes", 

	};

	private static String [] habitatEcologyList = new String[]{

		"Habitat",

		"Habitat & Ecology"

	};

	private static String [] generellDescriptionsList = new String[]{

		"Fossils",

		"Morphology and anatomy",

		"Morphology", 

		"Vegetative morphology and anatomy",

		"Flower morphology",

		"Palynology",  

		"Pollination",  

		"Pollen morphology",

		"Life cycle",

		"Fruits and embryology",

		"Dispersal",

		"Wood anatomy",  

		"Leaf anatomy",  

		"Chromosome numbers", 

		"Phytochemistry and Chemotaxonomy",

		"Phytochemistry",

		"Taxonomy",	

	};

	private static String [] descriptionFeatureList = new String[]{

		"lifeform", 

		"Bark",  

		"Indumentum",  

		"endophytic body",  

		"flowering buds",  

		"Branchlets",  

		"Branches",  

		"Branch",  

		"Flowering branchlets",

		"Trees",  

		"Twigs",  

		"stem",  

		"Stems",  

		"stem leaves", 

		"Leaves",

		"flower-bearing stems",  

		"Petiole",  

		"Petiolules",  

		"Leaflets", 

		"Thyrsus",  

		"Thyrses",  

		"Inflorescences",  

		"Inflorescence",

		"Young inflorescences", 

		"Bracts",  

		"Pedicels",  

		"flowering buds",  

		"scales",  

		"Buds",  

		"Flowers",  

		"Flower",  

		"Flowering",

		"Stigma",  

		"perianth",  

		"Sepals",  

		"Sepal",  

		"Outer Sepals",  

		"Axillary",  

		"cymes",  

		"Calyx",  

		"Petal",  

		"Petals",  

		"perigone tube",

		"Disc",  

		"corolla",  

		"Stamens",  

		"Staminodes",  

		"Ovary",  

		"Anthers",

		"anther",  

		"Pistil",  

		"Pistillode",  

		"Ovules",  

		"androecium",  

		"gynoecium",  

		"Filaments",  		

		"Style",  

		"annulus",  

		"female flowers",  

		"Male flowers",  

		"Female",  

		"Infructescences",    //order not consistent (sometimes before "Flowers")  

		"Fruit",  

		"Fruits",  

		"fruiting axes",  

		"drupes",  

		"Arillode",  

		"seed",  

		"Seeds",  

		"Seedling",  

		"flower tube", 

		"nutlets",  

		"pollen",  

		"secondary xylem",  

		"chromosome number",  

		"figure",  

		"fig",  

		"figs",  

	};

	public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){

		try {

			for (String featureString : featureStringList){

			UUID featureUuid;

			featureUuid = transformer.getFeatureUuid(featureString);

			Feature feature = (Feature)termService.find(featureUuid);

			if (feature != null){

				FeatureNode child = FeatureNode.NewInstance(feature);

				root.addChild(child);	

			}

		}

		} catch (UndefinedTransformerMethodException e) {

			logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");

		}

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		FloraMalesianaActivator me = new FloraMalesianaActivator();

		me.doImport(cdmDestination);

	}

}