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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.io.File;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.io.Reader;
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import java.io.UnsupportedEncodingException;
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import java.net.URI;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.zip.ZipEntry;
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import java.util.zip.ZipFile;
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import javax.xml.bind.JAXBContext;
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import javax.xml.bind.JAXBException;
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import javax.xml.bind.Unmarshaller;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import au.com.bytecode.opencsv.CSVParser;
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import au.com.bytecode.opencsv.CSVReader;
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import au.com.bytecode.opencsv.CSVWriter;
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import eu.etaxonomy.cdm.io.dwca.jaxb.Archive;
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import eu.etaxonomy.cdm.io.dwca.jaxb.ArchiveEntryBase;
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import eu.etaxonomy.cdm.io.dwca.jaxb.Extension;
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import eu.etaxonomy.cdm.io.dwca.out.DwcaMetaDataRecord;
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import eu.etaxonomy.cdm.io.stream.CsvStream;
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import eu.etaxonomy.cdm.io.stream.IReader;
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import eu.etaxonomy.cdm.io.stream.ListReader;
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import eu.etaxonomy.cdm.io.stream.terms.TermUri;
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/**
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* This class transforms a Darwin Core Archive zip file into a set of CSVReaderInputStreams.
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* For each data file included in the zip it creates one stream by evaluating the meta file.
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* Ecological metadata handling is still unclear.
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*
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* @author a.mueller
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* @since 17.10.2011
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*/
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public class DwcaZipToStreamConverter<STATE extends DwcaImportState> {
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private static Logger logger = Logger.getLogger(DwcaZipToStreamConverter.class);
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private final String META_XML = "meta.xml";
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protected static final boolean IS_CORE = true;
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private final List<TermUri> extensionList = Arrays.asList(
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TermUri.EOL_AGENT,
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TermUri.DWC_RESOURCE_RELATIONSHIP,
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TermUri.GBIF_TYPES_AND_SPECIMEN,
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TermUri.GBIF_VERNACULAR_NAMES,
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TermUri.GBIF_IDENTIFIER,
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TermUri.GBIF_SPECIES_PROFILE,
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TermUri.GBIF_REFERENCE,
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TermUri.GBIF_DESCRIPTION,
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TermUri.GBIF_DISTRIBUTION,
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TermUri.GBIF_IMAGE
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);
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private final URI dwcaZip;
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private final Map<String, DwcaMetaDataRecord> metaRecords = new HashMap<>();
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private Archive archive;
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/// ******************** FACTORY ********************************/
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public static DwcaZipToStreamConverter<DwcaImportState> NewInstance(URI dwcaZip){
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return new DwcaZipToStreamConverter(dwcaZip);
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}
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//************************ CONSTRUCTOR *********************************/
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public DwcaZipToStreamConverter(URI dwcaZip) {
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this.dwcaZip = dwcaZip;
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initArchive();
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}
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protected Archive getArchive(){
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return this.archive;
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}
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public CsvStream getCoreStream(STATE state) throws IOException{
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initArchive();
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ArchiveEntryBase core = archive.getCore();
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return makeStream(core, state);
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}
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public CsvStream getStream(String rowType, STATE state) throws IOException{
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initArchive();
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ArchiveEntryBase archiveEntry = null;
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List<Extension> extensions = archive.getExtension();
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for (Extension extension : extensions){
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if (rowType.equalsIgnoreCase(extension.getRowType())){
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archiveEntry = extension;
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break;
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}
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}
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return makeStream(archiveEntry, state);
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}
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public CsvStream getStream(TermUri rowType, STATE state) throws IOException{
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return getStream(rowType.getUriString(), state);
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}
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public IReader<CsvStream> getEntriesStream(STATE state){
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//core
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List<CsvStream> streamList = new ArrayList<>();
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try {
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if (state.getConfig().isDoTaxa()){
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streamList.add(getCoreStream(state)); //for taxa and names
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}
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} catch (IOException e) {
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String message = "Core stream not available for %s: %s";
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//FIXME fire event (also in following code)
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logger.warn(String.format(message, "taxa", e.getMessage()));
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state.setSuccess(false);
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}
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//core relationships
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try {
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if (state.getConfig().isDoTaxonRelationships()){
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streamList.add(getCoreStream(state)); //for taxon and name relations
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}
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} catch (IOException e) {
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String message = "Core stream not available for %s: %s";
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logger.warn(String.format(message, "taxon relations", e.getMessage()));
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state.setSuccess(false);
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}
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//extensions
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for (TermUri extension : extensionList){
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CsvStream extensionStream;
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try {
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if (state.getConfig().isDoExtensions()){
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extensionStream = getStream(extension, state);
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if (extensionStream != null){
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streamList.add(extensionStream);
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}
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}
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} catch (IOException e) {
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String message = "Extension stream not available for extension %s: %s";
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logger.warn(String.format(message, extension.getUriString(), e.getMessage()));
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state.setSuccess(false);
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}
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}
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IReader<CsvStream> result = new ListReader<>(streamList);
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return result;
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}
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/**
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* Creates the CsvStream for an archive entry. Returns null if archive entry is null.
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* @param archiveEntry
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* @param state
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* @return
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* @throws IOException
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* @throws UnsupportedEncodingException
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*/
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private CsvStream makeStream(ArchiveEntryBase archiveEntry, STATE state) throws IOException, UnsupportedEncodingException {
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if (archiveEntry == null){
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return null;
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}
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char fieldTerminatedBy = StringUtils.isEmpty(archiveEntry.getFieldsTerminatedBy()) ? CSVParser.DEFAULT_SEPARATOR : archiveEntry.getFieldsTerminatedBy().charAt(0);
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// default is a kind of 'null' quote, which tells opencsv to ignore the enclosing quotes
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char fieldsEnclosedBy = CSVWriter.NO_QUOTE_CHARACTER;
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if(state == null || !state.getConfig().isNoQuotes()) {
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fieldsEnclosedBy= StringUtils.isEmpty(archiveEntry.getFieldsEnclosedBy()) ? CSVParser.DEFAULT_QUOTE_CHARACTER: archiveEntry.getFieldsEnclosedBy().charAt(0);
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}
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boolean ignoreHeader = archiveEntry.getIgnoreHeaderLines();
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String linesTerminatedBy = archiveEntry.getLinesTerminatedBy();
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String encoding = archiveEntry.getEncoding();
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int skipLines = ignoreHeader? 1 : 0;
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String fileLocation = archiveEntry.getFiles().getLocation();
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InputStream coreCsvInputStream = makeInputStream(fileLocation);
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Reader coreReader = new InputStreamReader(coreCsvInputStream, encoding);
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CSVReader csvReader = new CSVReader(coreReader, fieldTerminatedBy,fieldsEnclosedBy, skipLines);
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CsvStream csvStream = new CsvStream(csvReader, archiveEntry, skipLines);
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// InputStream s;
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// s.
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return csvStream;
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}
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private void initArchive() {
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if (archive == null){
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try {
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InputStream metaInputStream = makeInputStream(META_XML);
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JAXBContext jaxbContext = JAXBContext.newInstance("eu.etaxonomy.cdm.io.dwca.jaxb");
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Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
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archive = (Archive)unmarshaller.unmarshal(metaInputStream);
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validateArchive(archive);
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} catch (IOException e) {
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throw new RuntimeException(e);
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} catch (JAXBException 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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private void validateArchive(Archive archive) {
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if (archive.getCore().getFieldsTerminatedBy() != null && archive.getCore().getFieldsTerminatedBy().length() > 1){
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if (archive.getCore().getFieldsTerminatedBy().equals("\\t") ){
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//TODO handle, TODO also handle other \xxx delimiter
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}else{
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throw new IllegalStateException("CsvReader does not allow field delimiters with more than 1 character. ");
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}
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}
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if (archive.getCore().getFieldsEnclosedBy() != null && archive.getCore().getFieldsEnclosedBy().length() > 1){
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throw new IllegalStateException("CsvReader does not allow field delimiters with more than 1 character");
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}
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}
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//
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// /**
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// * @return
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// * @throws IOException
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// */
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// private InputStream makeInputStream(String name) throws IOException {
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//
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// ZipInputStream zin = new ZipInputStream(dwcaZip.toURL().openStream());
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// ZipEntry ze = zin.getNextEntry();
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// while (!ze.getName().equals(name)) {
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// zin.closeEntry(); // not sure whether this is necessary
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// ze = zin.getNextEntry();
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// }
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//
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// CheckedInputStream cis = new CheckedInputStream(in, cksum)
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//
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// InputStream metaInputStream = zip.getInputStream(ze);
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// return metaInputStream;
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//
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// InputStream metaInputStream = zip.getInputStream(metaEntry);
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// return metaInputStream;
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// }
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//
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private InputStream makeInputStream(String name) throws IOException {
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File file = new File(dwcaZip);
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if (! file.isFile() || ! file.exists()){
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String message = "URI is not a file: %s";
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throw new IOException(String.format(message, dwcaZip.toString()));
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}
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ZipFile zip = new ZipFile(file, ZipFile.OPEN_READ);
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//Enumeration<? extends ZipEntry> zipEntries = zip.entries();
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//ze = new ZipEntry(name);
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ZipEntry metaEntry = zip.getEntry(name);
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//Lorna added this to deal with Scratchpads dwca.zip files which when unzipped have a directory dwca/ which contains the files
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if (metaEntry == null) {
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metaEntry = zip.getEntry("dwca/" + name);
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}
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if (metaEntry == null){
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String message = "Zip entry for %s not available";
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throw new IOException(String.format(message, name));
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}
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InputStream metaInputStream = zip.getInputStream(metaEntry);
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return metaInputStream;
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}
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}
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