EDIT

/**

* Copyright (C) 2009 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.io.dwca.in;

import java.io.File;

import java.io.IOException;

import java.io.InputStream;

import java.io.InputStreamReader;

import java.io.Reader;

import java.io.UnsupportedEncodingException;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import java.util.zip.ZipEntry;

import java.util.zip.ZipFile;

import javax.xml.bind.JAXBContext;

import javax.xml.bind.JAXBException;

import javax.xml.bind.Unmarshaller;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import au.com.bytecode.opencsv.CSVParser;

import au.com.bytecode.opencsv.CSVReader;

import au.com.bytecode.opencsv.CSVWriter;

import eu.etaxonomy.cdm.common.URI;

import eu.etaxonomy.cdm.io.dwca.jaxb.Archive;

import eu.etaxonomy.cdm.io.dwca.jaxb.ArchiveEntryBase;

import eu.etaxonomy.cdm.io.dwca.jaxb.Extension;

import eu.etaxonomy.cdm.io.dwca.out.DwcaMetaDataRecord;

import eu.etaxonomy.cdm.io.stream.CsvStream;

import eu.etaxonomy.cdm.io.stream.IReader;

import eu.etaxonomy.cdm.io.stream.ListReader;

import eu.etaxonomy.cdm.io.stream.terms.TermUri;

/**

 * This class transforms a Darwin Core Archive zip file into a set of CSVReaderInputStreams.

 * For each data file included in the zip it creates one stream by evaluating the meta file.

 * Ecological metadata handling is still unclear.

 *

 * @author a.mueller

 * @since 17.10.2011

 */

public class DwcaZipToStreamConverter<STATE extends DwcaImportState> {

	private static Logger logger = Logger.getLogger(DwcaZipToStreamConverter.class);

	private final String META_XML = "meta.xml";

	protected static final boolean IS_CORE = true;

	private final List<TermUri> extensionList = Arrays.asList(

			TermUri.EOL_AGENT,

			TermUri.DWC_RESOURCE_RELATIONSHIP,

			TermUri.GBIF_TYPES_AND_SPECIMEN,

			TermUri.GBIF_VERNACULAR_NAMES,

			TermUri.GBIF_IDENTIFIER,

			TermUri.GBIF_SPECIES_PROFILE,

			TermUri.GBIF_REFERENCE,

			TermUri.GBIF_DESCRIPTION,

			TermUri.GBIF_DISTRIBUTION,

			TermUri.GBIF_IMAGE

	);

	private final URI dwcaZip;

	private final Map<String, DwcaMetaDataRecord> metaRecords = new HashMap<>();

	private Archive archive;

/// ******************** FACTORY ********************************/

	public static DwcaZipToStreamConverter<DwcaImportState> NewInstance(URI dwcaZip){

		return new DwcaZipToStreamConverter(dwcaZip);

	}

//************************ CONSTRUCTOR *********************************/

	public DwcaZipToStreamConverter(URI dwcaZip) {

		this.dwcaZip = dwcaZip;

		initArchive();

	}

	protected Archive getArchive(){

			return this.archive;

	}

	public CsvStream getCoreStream(STATE state) throws IOException{

		initArchive();

		ArchiveEntryBase core = archive.getCore();

		return makeStream(core, state);

	}

	public CsvStream getStream(String rowType, STATE state) throws IOException{

		initArchive();

		ArchiveEntryBase archiveEntry = null;

		List<Extension> extensions = archive.getExtension();

		for (Extension extension : extensions){

			if (rowType.equalsIgnoreCase(extension.getRowType())){

				archiveEntry = extension;

				break;

			}

		}

		return makeStream(archiveEntry, state);

	}

	public CsvStream getStream(TermUri rowType, STATE state) throws IOException{

		return getStream(rowType.getUriString(), state);

	}

	public IReader<CsvStream> getEntriesStream(STATE state){

		//core

		List<CsvStream> streamList = new ArrayList<>();

		try {

			if (state.getConfig().isDoTaxa()){

			    streamList.add(getCoreStream(state)); //for taxa and names

			}

		} catch (IOException e) {

			String message = "Core stream not available for %s: %s";

			//FIXME fire event (also in following code)

			logger.warn(String.format(message, "taxa", e.getMessage()));

			state.setSuccess(false);

		}

		//core relationships

		try {

			if (state.getConfig().isDoTaxonRelationships()){

			    streamList.add(getCoreStream(state)); //for taxon and name relations

			}

		} catch (IOException e) {

			String message = "Core stream not available for %s: %s";

			logger.warn(String.format(message, "taxon relations", e.getMessage()));

			state.setSuccess(false);

		}

		//extensions

		for (TermUri extension : extensionList){

			CsvStream extensionStream;

			try {

	            if (state.getConfig().isDoExtensions()){

	                extensionStream = getStream(extension, state);

	                if (extensionStream != null){

	                    streamList.add(extensionStream);

	                }

	            }

			} catch (IOException e) {

				String message = "Extension stream not available for extension %s: %s";

				logger.warn(String.format(message, extension.getUriString(), e.getMessage()));

				state.setSuccess(false);

			}

		}

		IReader<CsvStream> result = new ListReader<>(streamList);

		return result;

	}

	/**

	 * Creates the CsvStream for an archive entry. Returns null if archive entry is null.

	 * @param archiveEntry

	 * @param state

	 * @return

	 * @throws IOException

	 * @throws UnsupportedEncodingException

	 */

	private CsvStream makeStream(ArchiveEntryBase archiveEntry, STATE state) throws IOException, UnsupportedEncodingException {

		if (archiveEntry == null){

			return null;

		}

		char fieldTerminatedBy = StringUtils.isEmpty(archiveEntry.getFieldsTerminatedBy()) ? CSVParser.DEFAULT_SEPARATOR : archiveEntry.getFieldsTerminatedBy().charAt(0);

		// default is a kind of 'null' quote, which tells opencsv to ignore the enclosing quotes

		char fieldsEnclosedBy = CSVWriter.NO_QUOTE_CHARACTER;

		if(state == null || !state.getConfig().isNoQuotes()) {

		        fieldsEnclosedBy= StringUtils.isEmpty(archiveEntry.getFieldsEnclosedBy()) ? CSVParser.DEFAULT_QUOTE_CHARACTER: archiveEntry.getFieldsEnclosedBy().charAt(0);

		}

		boolean ignoreHeader = archiveEntry.getIgnoreHeaderLines();

		String linesTerminatedBy = archiveEntry.getLinesTerminatedBy();

		String encoding = archiveEntry.getEncoding();

		int skipLines = ignoreHeader? 1 : 0;

		String fileLocation = archiveEntry.getFiles().getLocation();

		InputStream coreCsvInputStream = makeInputStream(fileLocation);

		Reader coreReader = new InputStreamReader(coreCsvInputStream, encoding);

		CSVReader csvReader = new CSVReader(coreReader, fieldTerminatedBy,fieldsEnclosedBy, skipLines);

		CsvStream csvStream = new CsvStream(csvReader, archiveEntry, skipLines);

		//		InputStream s;

//		s.

		return csvStream;

	}

	private void initArchive() {

		if (archive == null){

			try {

				InputStream metaInputStream = makeInputStream(META_XML);

				JAXBContext jaxbContext = JAXBContext.newInstance("eu.etaxonomy.cdm.io.dwca.jaxb");

				Unmarshaller unmarshaller =  jaxbContext.createUnmarshaller();

				archive = (Archive)unmarshaller.unmarshal(metaInputStream);

				validateArchive(archive);

			} catch (IOException e) {

				throw new RuntimeException(e);

			} catch (JAXBException e) {

				throw new RuntimeException(e);

			}

		}

	}

	private void validateArchive(Archive archive) {

		if (archive.getCore().getFieldsTerminatedBy() != null && archive.getCore().getFieldsTerminatedBy().length() > 1){

			if (archive.getCore().getFieldsTerminatedBy().equals("\\t") ){

				//TODO handle, TODO also handle other \xxx delimiter

			}else{

				throw new IllegalStateException("CsvReader does not allow field delimiters with more than 1 character. ");

			}

		}

		if (archive.getCore().getFieldsEnclosedBy() != null && archive.getCore().getFieldsEnclosedBy().length() > 1){

			throw new IllegalStateException("CsvReader does not allow field delimiters with more than 1 character");

		}

	}

//

//	/**

//	 * @return

//	 * @throws IOException

//	 */

//	private InputStream makeInputStream(String name) throws IOException {

//

//		ZipInputStream zin = new ZipInputStream(dwcaZip.toURL().openStream());

//		ZipEntry ze = zin.getNextEntry();

//		while (!ze.getName().equals(name)) {

//		    zin.closeEntry(); // not sure whether this is necessary

//		    ze = zin.getNextEntry();

//		}

//

//		CheckedInputStream cis = new CheckedInputStream(in, cksum)

//

//		InputStream metaInputStream = zip.getInputStream(ze);

//		return metaInputStream;

//

//		InputStream metaInputStream = zip.getInputStream(metaEntry);

//		return metaInputStream;

//	}

//

	private InputStream makeInputStream(String name) throws IOException {

		File file = new File(dwcaZip.getJavaUri());

		if (! file.isFile() || ! file.exists()){

			String message = "URI is not a file: %s";

			throw new IOException(String.format(message, dwcaZip.toString()));

		}

		ZipFile zip = new ZipFile(file, ZipFile.OPEN_READ);

		//Enumeration<? extends ZipEntry> zipEntries = zip.entries();

		//ze = new ZipEntry(name);

		ZipEntry metaEntry = zip.getEntry(name);

		//Lorna added this to deal with Scratchpads dwca.zip files which when unzipped have a directory dwca/ which contains the files

		if (metaEntry == null) {

			metaEntry = zip.getEntry("dwca/" + name);

		}

		if (metaEntry == null){

			String message = "Zip entry for %s not available";

			throw new IOException(String.format(message, name));

		}

		InputStream metaInputStream = zip.getInputStream(metaEntry);

		return metaInputStream;

	}

}