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/**
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* Copyright (C) 2009 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.dwca.in;
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import java.net.URI;
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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 eu.etaxonomy.cdm.api.service.IIdentifiableEntityService;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.dwca.TermUri;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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/**
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*
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* @author a.mueller
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*
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*/
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@Component
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public class DwcaImport extends CdmImportBase<DwcaImportConfigurator, DwcaImportState>{
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private static final Logger logger = Logger.getLogger(DwcaImport.class);
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@Override
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protected void doInvoke(DwcaImportState state) {
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URI source = state.getConfig().getSource();
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makeSourceRef(state);
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DwcaZipToStreamConverter<DwcaImportState> dwcaStreamConverter = DwcaZipToStreamConverter.NewInstance(source);
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IReader<CsvStream> zipEntryStream = dwcaStreamConverter.getEntriesStream(state);
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while (zipEntryStream.hasNext()){
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CsvStream csvStream = zipEntryStream.read();
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try {
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handleSingleZipEntry(state, csvStream);
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} catch (Exception e) {
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String message = "Exception (%s) occurred while handling zip entry %s";
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message = String.format(message, e.getMessage(), csvStream.toString());
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fireWarningEvent (message, csvStream.toString(), 14);
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}
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}
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state.finish();
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return;
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}
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/**
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* @param state
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* @param zipEntryStream
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*/
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private void handleSingleZipEntry(DwcaImportState state, CsvStream csvStream) {
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csvStream.addObservers(state.getConfig().getObservers());
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if (state.getConfig().isUsePartitions()){
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IPartitionableConverter<CsvStreamItem, IReader<CdmBase>, String> partitionConverter = getConverter(csvStream.getTerm(), state);
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if (partitionConverter == null){
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String warning = "No converter available for %s. Continue with next stream.";
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warning = String.format(warning, csvStream.getTerm());
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fireWarningEvent (warning, csvStream.toString(), 12);
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return;
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}
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int partitionSize = state.getConfig().getDefaultPartitionSize();
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StreamPartitioner<CsvStreamItem> partitionStream = new StreamPartitioner<CsvStreamItem>(csvStream,
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partitionConverter, state, partitionSize);// (csvStream, streamConverter,state 1000);
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int i = 1;
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while (partitionStream.hasNext()){
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//FIXME more generic handling of transactions
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TransactionStatus tx = startTransaction();
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try {
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IReader<MappedCdmBase> partStream = partitionStream.read();
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fireProgressEvent("Handel " + i + ". partition", i + ". partition");
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logger.info("Handel " + i++ + ". partition");
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String location = "Location: partition stream (TODO)";
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handleResults(state, partStream, location);
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commitTransaction(tx);
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} catch (Exception e) {
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String message = "An exception occurred while handling partition: " + e;
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String codeLocation;
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if (e.getStackTrace().length > 0){
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StackTraceElement el = e.getStackTrace()[0];
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codeLocation = el.getClassName()+ "." + el.getMethodName() + "(" + el.getLineNumber() + ")";
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}else{
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codeLocation = "No stacktrace";
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}
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message = message + " in: " + codeLocation;
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fireWarningEvent(message , String.valueOf(csvStream.getLine()) , 12);
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this.rollbackTransaction(tx);
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}
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}
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logger.debug("Partition stream is empty");
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}else {
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while (csvStream.hasNext()){
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TransactionStatus tx = startTransaction();
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CsvStreamItem item = csvStream.read();
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handleCsvStreamItem(state, item);
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commitTransaction(tx);
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}
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}
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finalizeStream(csvStream, state);
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}
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private void makeSourceRef(DwcaImportState state) {
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Reference<?> sourceRef = state.getConfig().getSourceReference();
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getReferenceService().saveOrUpdate(sourceRef);
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}
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// private void handlePartitionedStreamItem(DwcaImportState state, StreamPartitioner<CsvStreamItem> partitionStream) {
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// IPartitionableConverter<CsvStreamItem, IReader<CdmBase>, String> converter = getConverter(partitionStream.getTerm(), state);
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// if (converter == null){
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// state.setSuccess(false);
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// return;
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// }
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//
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// IReader<CsvStreamItem> lookaheadStream = partitionStream.getLookaheadReader();
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// Map<String, Set<String>> foreignKeys = converter.getPartitionForeignKeys(lookaheadStream);
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// IImportMapping mapping = state.getMapping();
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// IImportMapping partialMapping = mapping.getPartialMapping(foreignKeys);
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// state.loadRelatedObjects(partialMapping);
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//
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// ConcatenatingReader<MappedCdmBase> reader = new ConcatenatingReader<MappedCdmBase>();
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//
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// IReader<CsvStreamItem> inputStream = partitionStream.read();
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// while (inputStream.hasNext()){
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// IReader<MappedCdmBase> resultReader = converter.map(inputStream.read());
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// reader.add(resultReader);
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// }
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//
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// while (reader.hasNext()){
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// MappedCdmBase mappedCdmBase = (reader.read());
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// CdmBase cdmBase = mappedCdmBase.getCdmBase();
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// //locate
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// //TODO find a way to define the location
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// String location = "partitionStream";
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// //save
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// save(cdmBase, state, location);
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// //store in mapping
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// if (mappedCdmBase.getSourceId() != null && cdmBase.isInstanceOf(IdentifiableEntity.class)){
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// IdentifiableEntity<?> entity = CdmBase.deproxy(cdmBase, IdentifiableEntity.class);
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// String namespace = mappedCdmBase.getNamespace();
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// //TODO also store in partition mapping
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// state.putMapping(namespace,mappedCdmBase.getSourceId(), entity);
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// }
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// }
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// return;
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// }
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/**
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* @param state
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* @param item
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* @return
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*/
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private void handleCsvStreamItem(DwcaImportState state, CsvStreamItem item) {
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IConverter<CsvStreamItem, IReader<CdmBase>, String> converter = getConverter(item.term, state);
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if (converter == null){
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state.setSuccess(false);
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return;
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}
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IReader<MappedCdmBase> resultReader = converter.map(item);
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handleResults(state, resultReader, item.getLocation());
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return;
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}
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/**
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* @param state
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* @param item
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* @param resultReader
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*/
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private void handleResults(DwcaImportState state, IReader<MappedCdmBase> resultReader, String location) {
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while (resultReader.hasNext()){
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MappedCdmBase mappedCdmBase = resultReader.read();
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CdmBase cdmBase = mappedCdmBase.getCdmBase();
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save(cdmBase, state, location);
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if (mappedCdmBase.getSourceId() != null && cdmBase.isInstanceOf(IdentifiableEntity.class)){
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IdentifiableEntity<?> entity = CdmBase.deproxy(cdmBase, IdentifiableEntity.class);
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String namespace = mappedCdmBase.getNamespace();
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state.putMapping(namespace,mappedCdmBase.getSourceId(), entity);
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}
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}
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}
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private void finalizeStream(CsvStream csvStream, DwcaImportState state) {
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fireWarningEvent("Stream finished", csvStream.getFilesLocation(), 0);
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if (csvStream.getTerm().equals(TermUri.DWC_TAXON)){
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if (state.isTaxaCreated() == false){
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state.setTaxaCreated(true);
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}
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}
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}
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private void save(CdmBase cdmBase, DwcaImportState state, String location) {
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if (state.isCheck()){
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//do nothing
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}else{
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if (cdmBase == null){
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logger.warn("cdmBase is null");
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}
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//start preliminary for testing
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IIdentifiableEntityService service;
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try {
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if (cdmBase.isInstanceOf(IdentifiableEntity.class)){
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service = getServiceByClass(cdmBase.getClass());
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if (service != null){
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IdentifiableEntity<?> entity = CdmBase.deproxy(cdmBase, IdentifiableEntity.class);
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service.saveOrUpdate(entity);
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}
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}
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} catch (IllegalArgumentException e) {
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fireWarningEvent(e.getMessage(), location, 12);
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}
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// System.out.println(cdmBase.toString());
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//end preliminary
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//TODO
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}
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}
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private IPartitionableConverter<CsvStreamItem,IReader<CdmBase>, String> getConverter(TermUri namespace, DwcaImportState state) {
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if (namespace.equals(TermUri.DWC_TAXON)){
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if (! state.isTaxaCreated()){
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return new DwcTaxonCsv2CdmTaxonConverter(state);
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}else{
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return new DwcTaxonCsv2CdmTaxonRelationConverter(state);
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}
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}else if (namespace.equals(TermUri.GBIF_VERNACULAR_NAMES)){
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return new GbifVernacularNameCsv2CdmConverter(state);
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}else if (namespace.equals(TermUri.GBIF_DESCRIPTION)){
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return new GbifDescriptionCsv2CdmConverter(state);
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}else if (namespace.equals(TermUri.GBIF_DISTRIBUTION)){
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return new GbifDistributionCsv2CdmConverter(state);
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}else if (namespace.equals(TermUri.GBIF_REFERENCE)){
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return new GbifReferenceCsv2CdmConverter(state);
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}else{
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String message = "No converter available for %s";
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logger.error(String.format(message, namespace));
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return null;
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}
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}
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/**
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* Returns an appropriate service to persist data of a certain class.
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* If an appropriate service can't be found an {@link IllegalArgumentException} is thrown.
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*
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* TODO move to a more general place to make it available to everyone.
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*
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* @param app
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* @param clazz
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* @return
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*/
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protected IIdentifiableEntityService getServiceByClass(Class<?> clazz) throws IllegalArgumentException {
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if (clazz == null){
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//throw exception below
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}else if (TaxonBase.class.isAssignableFrom(clazz)){
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return this.getTaxonService();
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}else if (Classification.class.isAssignableFrom(clazz)){
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return this.getClassificationService();
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}else if (Reference.class.isAssignableFrom(clazz)){
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return this.getReferenceService();
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}else if (TaxonNameBase.class.isAssignableFrom(clazz)){
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return this.getNameService();
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}else if (DefinedTermBase.class.isAssignableFrom(clazz)){
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return this.getTermService();
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}else if (DescriptionBase.class.isAssignableFrom(clazz)){
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return this.getDescriptionService();
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}
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String warning = "Can't map class to API service: %s";
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warning = String.format(warning, (clazz == null ? "-" : clazz.getName()));
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throw new IllegalArgumentException(warning);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmImportBase#getFeature(eu.etaxonomy.cdm.io.common.ImportStateBase, java.util.UUID, java.lang.String, java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.common.TermVocabulary)
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*/
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//Make public to allow to use by converters
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@Override
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public Feature getFeature(DwcaImportState state, UUID uuid, String label, String description, String labelAbbrev, TermVocabulary<Feature> voc) {
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return super.getFeature(state, uuid, label, description, labelAbbrev, voc);
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}
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/**
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* Saves a new term. Immediate saving is required to avoid by Transient-Object-Exceptions.
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* @param newTerm
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*/
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public void saveNewTerm(DefinedTermBase newTerm) {
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getTermService().save(newTerm);
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}
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@Override
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protected boolean doCheck(DwcaImportState state) {
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return state.isCheck();
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}
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@Override
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protected boolean isIgnore(DwcaImportState state) {
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return false;
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}
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}
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