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.HashSet;

import java.util.List;

import java.util.Set;

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.events.IIoObserver;

import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver;

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

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

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

import eu.etaxonomy.cdm.io.markup.MarkupImportConfigurator;

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.Reference;

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

/**

 * @author a.mueller

 * @created 20.06.2008

 * @version 1.0

 */

public class FloraMalesianaVol13Activator {

	private static final Logger logger = Logger.getLogger(FloraMalesianaVol13Activator.class);

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

	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;

	static final URI fmSource13_small = EfloraSources.fm_13_small_families();

	static final URI fmSource13_large = EfloraSources.fm_13_large_families();

	static final URI fmSource12 = EfloraSources.fm_12();

	static final URI fmSource2_2 = EfloraSources.fm_2_2();

//	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();

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

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

	private boolean includeVol13_small = false;

	private boolean includeVol13_large = false;

	private boolean includeVol12 = true;

	private boolean includeVol2_2 = true;

	private boolean h2ForCheck = true;

	//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 CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	static boolean doPrintKeys = false;

	//taxa

	static final boolean doTaxa = true;

	private boolean replaceStandardKeyTitles = false;

	private IIoObserver observer = new LoggingIoObserver();

	private Set<IIoObserver> observerList = new HashSet<IIoObserver>();

	private void doImport(ICdmDataSource cdmDestination){

		observerList.add(observer);

		if (h2ForCheck && cdmDestination.getDatabaseType().equals(CdmDestinations.localH2().getDatabaseType())){

			check = CHECK.CHECK_ONLY;

		}

		//make Source

		URI source = fmSource13_small;

		MarkupImportConfigurator markupConfig= MarkupImportConfigurator.NewInstance(source, cdmDestination);

		markupConfig.setClassificationUuid(classificationUuid);

		markupConfig.setDoTaxa(doTaxa);

		markupConfig.setCheck(check);

		markupConfig.setDoPrintKeys(doPrintKeys);

		markupConfig.setDbSchemaValidation(hbm2dll);

		markupConfig.setObservers(observerList);

		markupConfig.setReplaceStandardKeyTitles(replaceStandardKeyTitles);

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

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

		//Vol13_2

		if (includeVol13_large){

			System.out.println("\nStart import from ("+ fmSource13_large.toString() + ") ...");

			source = fmSource13_large;

			markupConfig.setSource(source);

			myImport.invoke(markupConfig);

			System.out.println("End import from ("+ fmSource13_large.toString() + ")...");

		}

		//Vol13_1

		if (includeVol13_small){

			System.out.println("\nStart import from ("+ fmSource13_small.toString() + ") ...");

			source = fmSource13_small;

			markupConfig.setSource(source);

			myImport.invoke(markupConfig);

			System.out.println("End import from ("+ fmSource13_small.toString() + ")...");

		}

		//Vol12

		if (includeVol12){

			source = fmSource12;

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

			markupConfig.setSource(source);

			myImport.invoke(markupConfig);

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

		}

		//Vol_2_2

		if (includeVol2_2){

			source = fmSource2_2;

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

			markupConfig.setSource(source);

			myImport.invoke(markupConfig);

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

		}

//		makeGeoService();

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

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

		//check keys

		if (doPrintKeys){

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

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

			for(PolytomousKey key : keys){

				key.print(System.out);

				System.out.println();

			}

			myImport.getCdmAppController().commitTransaction(tx);

		}

	}

	private Reference getSourceReference(String string) {

		Reference 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(generellDescriptionsUpToAnatomyList, root, transformer, service);

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

		addFeataureNodesByStringList(anatomySubfeatureList, newNode, transformer, service);

		newNode = addFeataureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service);

		addFeataureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service);

		newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, 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 [] generellDescriptionsUpToAnatomyList = new String[]{

		"Fossils",

		"Morphology and anatomy",

		"Morphology", 

		"Vegetative morphology and anatomy",

	};

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

		"Leaf anatomy",

		"Wood anatomy"

	};

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

		"Flower morphology",

		"Palynology",  

		"Pollination",  

		"Pollen morphology",

		"embryology",

		"cytology",

		"Life cycle",

		"Fruits and embryology",

		"Dispersal",

		"Chromosome numbers", 

		"Phytochemistry and Chemotaxonomy",

	};

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

		"Alkaloids",

		"Iridoid glucosides",

		"Leaf phenolics",

		"Storage products of seeds",

		"Aluminium",

		"Chemotaxonomy",

	};

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

		"Phytochemistry",

		"Taxonomy",

		"history",

		"cultivation",

		"Notes"

	};

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

		"lifeform", 

		"Bark",

		//new

		"wood",

		"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", 

		"Male inflorescences", 

		"Female inflorescences", 

		"Bracts",  

		"Pedicels",  

		"flowering buds",  

		"scales",  

		"Buds",  

		"Flowers",  

		"Flower",  

		"Flowering",

		"Stigma",  

		"perianth",  

		"Sepals",  

		"Sepal",  

		"Outer Sepals",  

		"Axillary",  

		"cymes",  

		"Calyx",  

		"Petal",  

		"Petals",

		"perigone",

		"perigone lobes",

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

		FeatureNode lastChild = null;

		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");

		}

		return lastChild;

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		FloraMalesianaVol13Activator me = new FloraMalesianaVol13Activator();

		me.doImport(cdmDestination);

	}

}