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.wp6.diptera;

import java.io.File;

import java.io.FileInputStream;

import java.io.InputStream;

import java.io.InputStreamReader;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.springframework.transaction.TransactionStatus;

import au.com.bytecode.opencsv.CSVReader;

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

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

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

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

import eu.etaxonomy.cdm.model.agent.Institution;

import eu.etaxonomy.cdm.model.occurrence.Collection;

import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

/**

 * @author a.mueller

 * @date 07.04.2010

 *

 */

public class DipteraCollectionImport {

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

	public static final File acronymsFile = new File("src/main/resources/collections/Acronyms.tab");

	//datasource for use from local main()

	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();

	public ImportResult invoke(ICdmDataSource dataSource) {

	    ImportResult result = new ImportResult();

		CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);

		//create collections

		TransactionStatus tx = cdmApp.startTransaction();

		Map<String, Collection> colletionMap = createCollections(cdmApp);

		//add collections to specimen

		addCollectionsToSpecimen(cdmApp, colletionMap);

		cdmApp.commitTransaction(tx);

		return result;

	}

	/**

	 * @param cdmApp

	 * @param colletionMap

	 */

	private void addCollectionsToSpecimen(CdmApplicationController cdmApp, Map<String, Collection> colletionMap) {

		List<DerivedUnit> specimens = cdmApp.getOccurrenceService().list(DerivedUnit.class, null, null, null, null);

		for (SpecimenOrObservationBase<?> specOrObservBase : specimens){

			if (specOrObservBase.getRecordBasis().isPreservedSpecimen()){

				handleSingleSpecimen((DerivedUnit)specOrObservBase, colletionMap);

			}else{

				logger.warn("There are specimenOrObservationBase objects which are not of class Specimen. This is probably an error.");

			}

		}

		List<SpecimenOrObservationBase> specimenList = new ArrayList<SpecimenOrObservationBase>(specimens);

		cdmApp.getOccurrenceService().save(specimenList);

	}

	/**

	 * @param specimen

	 * @param colletionMap

	 */

	private void handleSingleSpecimen(DerivedUnit specimen, Map<String, Collection> collectionMap) {

		String titleCache = specimen.getTitleCache();

		String collectionCode = getCollectionCode(titleCache);

		if (StringUtils.isBlank(collectionCode)){

			logger.warn("Collection code is empty for: " + titleCache);

		}else{

			Collection collection = collectionMap.get(collectionCode);

			if (collection != null){

				specimen.setCollection(collection);

			}else{

				logger.warn("Collection not found for code: " +  collectionCode + "; titleCache: " +  titleCache);

			}

		}

	}

	/**

	 * @param titleCache

	 * @return

	 */

	private String getCollectionCode(String titleCache) {

		String result = titleCache.trim();

		result = replaceBracket(result);

		result = replaceLastFullStop(result);

		result = replaceLastQuestionMark(result);

		result = parseLastUpperCase(result);

		return result;

	}

	/**

	 * @param result

	 * @return

	 */

	private String parseLastUpperCase(String string) {

		String result = "";

		String tmpString = string;

		int pos = tmpString.lastIndexOf(" ");

		if (pos>-1){

			tmpString = tmpString.substring(pos+1);

		}

		while (tmpString.length() > 0){

			int len = tmpString.length();

			char lastChar = tmpString.charAt(len-1);

			if (Character.isUpperCase( lastChar)){

				result = lastChar + result;

			}else{

				if (result.length() > 0){

					logger.warn("Collection code is not space separated: " + string);

				}

				break;

			}

			//remove last character

			tmpString = tmpString.substring(0, tmpString.length()-1);

		}

		return result;

	}

	/**

	 * @param result

	 * @return

	 */

	private String replaceLastQuestionMark(String string) {

		if (string.endsWith("?")){

			string = string.substring(0,string.length()-1).trim();

		}

		return string;

	}

	/**

	 * @param result

	 * @return

	 */

	private String replaceLastFullStop(String string) {

		if (string.endsWith(".")){

			string = string.substring(0,string.length()-1).trim();

		}

		return string;

	}

	/**

	 * @param result

	 * @return

	 */

	private String replaceBracket(String string) {

		if (string.endsWith("]")){

			int pos  = string.indexOf("[");

			if (pos >0){

				string = string.substring(0, pos).trim();

			}else{

				logger.warn("Closing bracket has no opening bracket in: " + string);

			}

		}

		return string;

	}

	/**

	 * @param cdmApp

	 */

	private Map<String, Collection> createCollections(CdmApplicationController cdmApp) {

		Map<String, Collection> collectionMap = new HashMap<String, Collection>();

		List<String[]> lines = getLines();

		for (String[] line:lines){

			Collection collection = makeLine(line);

			collectionMap.put(collection.getCode(), collection);

		}

		cdmApp.getCollectionService().save(collectionMap.values());

//			for (Collection collection: collectionMap.values()){

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

//			}

		return collectionMap;

	}

	private Collection makeLine(String[] line) {

		String code = line[0];

		String instituteName = line[1];

		String lowerInstitutionName = line[2];

		String higherInstitutionName = line[3];

		String location = line[4];

		String country = line[5];

		//create objects

		Collection collection = Collection.NewInstance();

		collection.setCode(code);

		Institution institution = Institution.NewInstance();

		institution.setCode(code);

		institution.setName(instituteName);

		if (StringUtils.isNotBlank(lowerInstitutionName)){

			Institution lowerInstitution = Institution.NewInstance();

			lowerInstitution.setName(lowerInstitutionName);

			lowerInstitution.setIsPartOf(institution);

		}

		if (StringUtils.isNotBlank(higherInstitutionName)){

			Institution higherInstitution = Institution.NewInstance();

			higherInstitution.setName(higherInstitutionName);

			institution.setIsPartOf(higherInstitution);

		}

		collection.setInstitute(institution);

		String locationAndCountry = CdmUtils.concat("/", location, country);

		collection.setTownOrLocation(locationAndCountry);

		String titleCache = CdmUtils.concat(", ", new String[]{instituteName, lowerInstitutionName, higherInstitutionName, location, country});

		collection.setTitleCache(titleCache, true);

		return collection;

	}

	private List<String[]> getLines() {

		List<String[]> result = new ArrayList<String[]>();

		try {

			InputStream inStream = new FileInputStream(acronymsFile);

			InputStreamReader inputStreamReader = new InputStreamReader(inStream, "UTF8");

			CSVReader reader = new CSVReader(inputStreamReader, '\t');

			String [] nextLine = reader.readNext();

			while ((nextLine = reader.readNext()) != null) {

				if (nextLine.length == 0){

					continue;

				}

				result.add(nextLine);

			}

			return result;

		} catch (Exception e) {

			logger.error(e + " " + e.getCause() + " " + e.getMessage());

			for(StackTraceElement ste : e.getStackTrace()) {

				logger.error(ste);

			}

			throw new RuntimeException(e);

		}

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		try {

			DipteraCollectionImport collectionImport = new DipteraCollectionImport();

			collectionImport.invoke(cdmDestination);

//			String titleCache = "Peru. Mouth of Rio Pachitea. ST 2R SMT. [fig. of male abdomen]";

//			String collectionCode = collectionImport.getCollectionCode(titleCache);

//			System.out.println(collectionCode);

		} catch (Exception e) {

			e.printStackTrace();

			System.exit(-1);

		}

	}

}