EDIT

/**

* Copyright (C) 2008 EDIT

* European Distributed Institute of Taxonomy 

* http://www.e-taxonomy.eu

*/

package eu.etaxonomy.cdm.io.jaxb;

import java.io.File;

import java.net.URI;

import java.net.URISyntaxException;

import java.util.Collection;

import java.util.List;

import java.util.Map;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

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

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

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.media.Media;

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

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

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

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

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

/**

 * @author a.babadshanjan

 * @created 13.11.2008

 */

@Component

public class JaxbImport extends CdmIoBase<IImportConfigurator> implements ICdmIO<IImportConfigurator> {

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

	private CdmDocumentBuilder cdmDocumentBuilder = null;

    /** Reads data from an XML file and stores them into a CDM DB.

     * 

     * @param config

     * @param stores (not used)

     */

	@Override

	protected boolean doInvoke(IImportConfigurator config,

			Map<String, MapWrapper<? extends CdmBase>> stores) {

		boolean success = true;

        URI uri = null;

		JaxbImportConfigurator jaxbImpConfig = (JaxbImportConfigurator)config;

//    	String dbname = jaxbImpConfig.getDestination().getDatabase();

    	String urlFileName = (String)config.getSource();

		logger.debug("urlFileName: " + urlFileName);

    	try {

    		uri = new URI(urlFileName);

			logger.debug("uri: " + uri.toString());

    	} catch (URISyntaxException ex) {

			logger.error("File not found");

			return false;

    	}

		logger.info("Deserializing file " + urlFileName + " to DB " ); //+ dbname

		DataSet dataSet = new DataSet();

        // unmarshalling XML file

		try {

			cdmDocumentBuilder = new CdmDocumentBuilder();

			logger.info("Unmarshalling file: " + urlFileName);

			File file = new File(uri);

			logger.debug("Absolute path: " + file.getAbsolutePath());

			dataSet = cdmDocumentBuilder.unmarshal(dataSet, file);

		} catch (Exception e) {

			logger.error("Unmarshalling error");

			e.printStackTrace();

		} 

		// save data in DB

		logger.info("Saving data to DB: " ); //+ dbname

		success = saveData(jaxbImpConfig, dataSet);

		return success;

	}

	/**  Saves data in DB */

	private boolean saveData (JaxbImportConfigurator jaxbImpConfig, DataSet dataSet) {

		boolean ret = true;

		Collection<TaxonBase> taxonBases;

		List<? extends Agent> agents;

		List<DefinedTermBase> terms;

		List<ReferenceBase> references;

		List<TaxonNameBase> taxonomicNames;

		List<DescriptionBase> descriptions;

		List<ReferencedEntityBase> referencedEntities;

		List<SpecimenOrObservationBase> occurrences;

		List<VersionableEntity> featureData;

//		List<VersionableEntity> featureData;

		List<Media> media;

		List<LanguageStringBase> languageData;

		List<TermVocabulary<DefinedTermBase>> termVocabularies;

		List<HomotypicalGroup> homotypicalGroups;

		// Get an app controller that omits term loading

		// CdmApplicationController.getCdmAppController(boolean createNew, boolean omitTermLoading){

//		CdmApplicationController appCtr = jaxbImpConfig.getCdmAppController(false, true);

		//TransactionStatus txStatus = appCtr.startTransaction();

		TransactionStatus txStatus = null;

		// Have single transactions per service save call. Otherwise, getting

		// H2 HYT00 error (timeout locking table DEFINEDTERMBASE) when running from editor.

		// If data of a certain type, such as terms, are not saved here explicitly, 

		// then only those data of this type that are referenced by other objects are saved implicitly.

		// For example, if taxa are saved all other data referenced by those taxa, such as synonyms, 

		// are automatically saved as well.

		if ((jaxbImpConfig.isDoTermVocabularies() == true) 

				&& (termVocabularies = dataSet.getTermVocabularies()).size() > 0) {

			txStatus = startTransaction();

			ret &= saveTermVocabularies(termVocabularies);

			commitTransaction(txStatus);

		}

		if ((jaxbImpConfig.isDoTerms() == true)

				&& (terms = dataSet.getTerms()).size() > 0) {

			txStatus = startTransaction();

			ret &= saveTerms(terms);

			commitTransaction(txStatus);

		}

		// TODO: Have separate data save methods

		txStatus = startTransaction();

		try {

			if (jaxbImpConfig.isDoLanguageData() == true) {

				if ((languageData = dataSet.getLanguageData()).size() > 0) {

					logger.info("Language data: " + languageData.size());

					getTermService().saveLanguageDataAll(languageData);

				}

			}

		} catch (Exception ex) {

			logger.error("Error saving language data");

			ret = false;

		}

		commitTransaction(txStatus);

		txStatus = startTransaction();

		try {

			if (jaxbImpConfig.isDoAuthors() == true) {

				if ((agents = dataSet.getAgents()).size() > 0) {

					logger.info("Agents: " + agents.size());

					getAgentService().saveAgentAll(agents);

				}

			}

		} catch (Exception ex) {

			logger.error("Error saving agents");

			ret = false;

		}

		commitTransaction(txStatus);

		txStatus = startTransaction();

		try {

			if (jaxbImpConfig.getDoReferences() != IImportConfigurator.DO_REFERENCES.NONE) {

				if ((references = dataSet.getReferences()).size() > 0) {

					logger.info("References: " + references.size());

					getReferenceService().saveReferenceAll(references);

				}

			}

		} catch (Exception ex) {

			logger.error("Error saving references");

			ret = false;

		}

		commitTransaction(txStatus);

		txStatus = startTransaction();

		try {

			if (jaxbImpConfig.isDoTaxonNames() == true) {

				if ((taxonomicNames = dataSet.getTaxonomicNames()).size() > 0) {

					logger.info("Taxonomic names: " + taxonomicNames.size());

					getNameService().saveTaxonNameAll(taxonomicNames);

				}

			}

		} catch (Exception ex) {

			logger.error("Error saving taxon names");

			ret = false;

		}

		commitTransaction(txStatus);

		txStatus = startTransaction();

		try {

			if (jaxbImpConfig.isDoHomotypicalGroups() == true) {

				if ((homotypicalGroups = dataSet.getHomotypicalGroups()).size() > 0) {

					logger.info("Homotypical groups: " + homotypicalGroups.size());

					getNameService().saveAllHomotypicalGroups(homotypicalGroups);

				}

			}

		} catch (Exception ex) {

			logger.error("Error saving homotypical groups");

			ret = false;

		}

		commitTransaction(txStatus);

		txStatus = startTransaction();

		// Need to get the taxa and the synonyms here.

		try {

			if (jaxbImpConfig.isDoTaxa() == true) {

				if ((taxonBases = dataSet.getTaxonBases()).size() > 0) {

					logger.info("Taxon bases: " + taxonBases.size());

					getTaxonService().saveTaxonAll(taxonBases);

				}

			}

		} catch (Exception ex) {

			logger.error("Error saving taxa");

			ret = false;

		}

		commitTransaction(txStatus);

		txStatus = startTransaction();

		// NomenclaturalStatus, TypeDesignations

		try {

			if (jaxbImpConfig.isDoReferencedEntities() == true) {

				if ((referencedEntities = dataSet.getReferencedEntities()).size() > 0) {

					logger.info("Referenced entities: " + referencedEntities.size());

					getNameService().saveReferencedEntitiesAll(referencedEntities);

				}

			}

		} catch (Exception ex) {

			logger.error("Error saving referenced entities");

			ret = false;

		}

		commitTransaction(txStatus);

		// TODO: Implement dataSet.getDescriptions() and IDescriptionService.saveDescriptionAll()

//		if ((descriptions = dataSet.getDescriptions()) != null) {

//		logger.info("Saving " + descriptions.size() + " descriptions");

//		getDescriptionService().saveDescriptionAll(descriptions);

//		}

		txStatus = startTransaction();

		try {

			if (jaxbImpConfig.isDoOccurrence() == true) {

				if ((occurrences = dataSet.getOccurrences()).size() > 0) {

					logger.info("Occurrences: " + occurrences.size());

					getOccurrenceService().saveSpecimenOrObservationBaseAll(occurrences);

				}

			}

		} catch (Exception ex) {

			logger.error("Error saving occurrences");

			ret = false;

		}

		commitTransaction(txStatus);

		txStatus = startTransaction();

		try {

			if (jaxbImpConfig.isDoFeatureData() == true) {

				if ((featureData = dataSet.getFeatureData()).size() > 0) {

					logger.info("Feature data: " + featureData.size());

					getDescriptionService().saveFeatureDataAll(featureData);

				}

			}

		} catch (Exception ex) {

			logger.error("Error saving feature data");

			ret = false;

		}

		commitTransaction(txStatus);

		txStatus = startTransaction();

		try {

			if (jaxbImpConfig.isDoMedia() == true) {

				if ((media = dataSet.getMedia()).size() > 0) {

					logger.info("Media: " + media.size());

					getMediaService().saveMediaAll(media);

				}

			}

		} catch (Exception ex) {

			logger.error("Error saving media");

			ret = false;

		}

		commitTransaction(txStatus);

//		commitTransaction(txStatus);

		logger.info("All data saved");

		return ret;

	}

	private boolean saveTermVocabularies(

			List<TermVocabulary<DefinedTermBase>> termVocabularies) {

		boolean success = true;

		logger.info("Term vocabularies: " + termVocabularies.size());

		try {

			getTermService().saveTermVocabulariesAll(termVocabularies);

		} catch (Exception ex) {

			logger.error("Error saving term vocabularies");

			success = false;

		}

		return success;

	}

	private boolean saveTerms(List<DefinedTermBase> terms) {

		boolean success = true;

		logger.info("Terms: " + terms.size());

		try {

			getTermService().saveTermsAll(terms);

		} catch (Exception ex) {

			logger.error("Error saving terms");

			success = false;

		}

		return success;

	}

	@Override

	protected boolean doCheck(IImportConfigurator config) {

		boolean result = true;

		logger.warn("No check implemented for Jaxb import");

		return result;

	}

	@Override

	protected boolean isIgnore(IImportConfigurator config) {

		return false;

	}

}