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/**
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* Copyright (C) 2017 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.identifier;
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import java.io.File;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import au.com.bytecode.opencsv.CSVReader;
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import eu.etaxonomy.cdm.io.common.SimpleImport;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Identifier;
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import eu.etaxonomy.cdm.model.common.TermType;
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/**
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* Imports identifiers for a certain {@link IdentifiableEntity} class from a csv
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* file. The class and the identifier type are defined in the configurator.
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*
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* The csv file has to follow the following format:
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* <BR><BR>
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* 1. field: uuid of the {@link IdentifiableEntity} of class defined in configurator<BR>
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* 2. The value of the identifier (of type defined in configurator)<BR><BR>
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*
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* NOTE: This import was first written for #6542
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* NOTE 2: TODO It was observed that the last line was not imported.
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*
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* @author a.mueller
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* @date 25.03.2017
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*/
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@Component
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public class IdentifierImport
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extends SimpleImport<IdentifierImportConfigurator, File>{
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private static final long serialVersionUID = 5797541146159665997L;
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private static Logger logger = Logger.getLogger(IdentifierImport.class);
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/**
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* {@inheritDoc}
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*/
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@Override
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protected void doInvoke(IdentifierImportConfigurator config) {
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try {
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InputStreamReader inputReader = config.getSource();
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CSVReader csvReader = new CSVReader(inputReader, ';');
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List<String[]> lines = csvReader.readAll();
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if (lines.isEmpty()){
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logger.info("Import file is empty");
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csvReader.close();
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return;
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}
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@SuppressWarnings("rawtypes")
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Set<IdentifiableEntity> entitiesToSave = new HashSet<>();
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UUID identifierTypeUuid = config.getIdentifierTypeUuid();
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DefinedTermBase<?> identifierType = getTermService().find(identifierTypeUuid);
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if (identifierType == null || identifierType.getTermType() != TermType.IdentifierType){
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logger.warn("IdentifierType not recognized. Skip import");
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csvReader.close();
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return;
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}
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DefinedTerm idType = CdmBase.deproxy(identifierType, DefinedTerm.class);
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int i = 0;
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for (String[] strs : lines){
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IdentifiableEntity<?> entity = handleSingleLine(config, strs, idType, i);
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if (entity != null){
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entitiesToSave.add(entity);
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}
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i++;
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}
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csvReader.close();
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//not needed as the objects update automatically during transactions in handleSingleLine()
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// getCommonService().saveOrUpdate(entitiesToSave);
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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/**
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* @param config configurator
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* @param strs text array for given line
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* @param i line counter
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* @return
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*/
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private IdentifiableEntity<?> handleSingleLine(IdentifierImportConfigurator config,
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String[] strs, DefinedTerm idType, int i) {
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//no data
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if (strs.length < 1){
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String message = String.format(
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"No data available in line %d. Skipped", i);
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logger.warn(message);
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return null;
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}
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//entity uuid
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String uuidStr = strs[0];
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UUID uuid;
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try {
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uuid = UUID.fromString(uuidStr);
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} catch (Exception e) {
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String message = String.format(
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"Entity identifier not recognized as UUID in line %d. Skipped. Value was: %s", i, uuidStr);
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logger.warn(message);
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return null;
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}
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TransactionStatus tx = this.startTransaction();
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IdentifiableEntity<?> entity = getEntityFromRepository(config, uuid);
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if (entity == null){
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String message = String.format(
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"Entity for uuid %s could not be found in line %d. Skipped", uuid.toString(), i);
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logger.warn(message);
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return null;
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}
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//identifier value
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if (strs.length < 2){
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String message = String.format(
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"Record in line %d has no identifier value information. Skipped.", i);
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logger.warn(message);
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this.commitTransaction(tx);
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return null;
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}
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String value = null;
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if (isNotBlank(strs[1])){
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value = strs[1];
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}else if (config.isIgnoreEmptyIdentifier()){
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String message = String.format(
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"Record in line %d has empty identifier value information. Skipped.", i);
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logger.debug(message);
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this.commitTransaction(tx);
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return null;
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}
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Identifier<?> identifier = Identifier.NewInstance(value, idType);
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entity.addIdentifier(identifier);
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this.commitTransaction(tx);
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return entity;
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}
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private IdentifiableEntity<?> getEntityFromRepository(IdentifierImportConfigurator config, UUID uuid) {
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IdentifiableEntity<?> result = getCommonService().find(config.getCdmClass(), uuid);
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return result;
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}
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}
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