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Revision f104a204

Added by Andreas Müller almost 2 years ago

ID f104a2042a2efc8807c11f602799d182453361f4
Parent 45356f85
Child 98768399

cleanup

     //      this.workDone = this.workDone +  work;
+        }
         @Override
         public void internalWorked(double work) {
             computeWorked(work);
-...
             return result;
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public void waitForFeedback() {
             if(feedbackLock == null) {
-...
+            }
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public void setFeedback(Serializable feedback) {
             synchronized (feedbackLock) {
-...
+            }
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public Serializable getFeedback() {
             return feedback;
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public boolean getIsWaitingForFeedback() {
             return isWaitingForFeedback;
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public void waitForFeedback(long feedbackWaitTimeout) {
             if(feedbackWaitTimeout <= 0 ) {
-...
             waitForFeedback();
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public boolean hasFeedbackWaitTimedOut() {
            long now = System.currentTimeMillis();
            return isWaitingForFeedback && (now - feedbackWaitStartTime > feedbackWaitTimeout);
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public String getOwner() {
             return owner;
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public void setOwner(String owner) {
             this.owner = owner;
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public void interrupt() {
             // do nothing
+        }
+    }
+    }

     /**
+     *
      */
     * Copyright (C) 2015 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.common.monitor;
     import java.io.Serializable;
     /**
      * Empty default implementation
+     *
-...
     		//  do nothing
+    	}
         /**
          * {@inheritDoc}
          */
         @Override
         public void waitForFeedback() {
             //  do nothing
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public void setFeedback(Serializable feedback) {
             //  do nothing
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public Serializable getFeedback() {
             return null;
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public boolean getIsWaitingForFeedback() {
             return false;
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public void waitForFeedback(long feedbackWaitTimeout) {
         //  do nothing
             //  do nothing
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public boolean hasFeedbackWaitTimedOut() {
             return false;
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public String getOwner() {
             return null;
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public void setOwner(String owner) {
             //  do nothing
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public void interrupt() {
             //  do nothing
+        }
+    }
+    }

     /**
      * @author a.mueller
      * @since 14.03.2017
+     *
      */
     public class EmptyImportState<CONFIG extends ImportConfiguratorBase, IO extends CdmImportBase>
             extends ImportStateBase<CONFIG, IO> {
         /**
          * @param config
          */
         protected EmptyImportState(CONFIG config) {
             super(config);
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public CONFIG getConfig() {
             return super.getConfig();
+        }
+    }
+    }

     /**
      * @author a.mueller
      * @since 14.03.2017
+     *
      */
     public abstract class SimpleImportConfiguratorBase<SOURCE extends Object>
             extends ImportConfiguratorBase<EmptyImportState<SimpleImportConfiguratorBase,?>, SOURCE>{
         private static final long serialVersionUID = 5310312930219876822L;
         /**
          * @param transformer
          */
         protected SimpleImportConfiguratorBase(SOURCE source, ICdmDataSource destination, IInputTransformer transformer) {
             super(transformer);
             setSource(source);
             setDestination(destination);
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         public EmptyImportState getNewState() {
             return new EmptyImportState(this);
+        }
+    }
+    }

cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/in/CsvImportBase.java
109	109	} catch (IOException e) {
110	110	throw new RuntimeException(e);
111	111	}
112
113	112	}
114	113
115	114	private TransactionStatus startNewTransaction(STATE state, TransactionStatus tx) {
...	...
214	213	return sourceRef;
215	214	}
216	215
217		/**
218		* {@inheritDoc}
219		*/
220	216	@Override
221	217	protected boolean doCheck(STATE state) {
222	218	return true;
223	219	}
224	220
225		/**
226		* {@inheritDoc}
227		*/
228	221	@Override
229	222	protected boolean isIgnore(STATE state) {
230	223	return false;
231	224	}
232		}
	225	}

     * 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.csv.redlist.demo;
     import java.io.ByteArrayOutputStream;
-...
     import java.util.UUID;
     import org.apache.commons.lang.StringUtils;
     import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
     import org.apache.logging.log4j.LogManager;
     import org.apache.logging.log4j.Logger;
     import org.springframework.stereotype.Component;
     import org.springframework.transaction.TransactionStatus;
-...
     import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
     import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
     /**
      * @author a.oppermann
      * @since 18.10.2012
      */
     @Component
     public class CsvDemoExport extends CsvDemoBase {
-...
+                        }
                         break;
                     case EXPORT_DATA:
                         exportStream = new ByteArrayOutputStream();;
                         exportStream = new ByteArrayOutputStream();
                         writer = new PrintWriter(exportStream);
                         break;
                     default :
-...
     	        this.clearExistingRecordIds();
+    	    }
     //	    commitTransaction(txStatus);
     	    return;
+    	}
         /**
          * @param state
          * @param config
          * @param txStatus
          * @param classificationSet
          * @param recordList
          */
         private void performJsonXMLPagination(CsvDemoExportState state, CsvDemoExportConfigurator config,
                 TransactionStatus txStatus, Set<Classification> classificationSet, List<CsvDemoRecord> recordList) {
             // TODO Auto-generated method stub
             Classification classification = null;
             for(Classification c : classificationSet){
                 classification = c;
-...
             commitTransaction(txStatus);
+        }
         /**
          * @param state
          * @param config
          * @param txStatus
          * @param classificationSet
          * @param progressMonitor
          * @param writer
          * @return
          */
     	private void performCSVExport(CsvDemoExportState state, CsvDemoExportConfigurator config,
     	        TransactionStatus txStatus, Set<Classification> classificationSet, IProgressMonitor progressMonitor,
     	        PrintWriter writer) {
-...
+    	    }
+    	}
         //TODO: Exception handling
     	/**
+    	 *
     	 * @param config
     	 * @return
     	 */
     	protected Set<Classification> assembleClassificationSet(CsvDemoExportConfigurator config){
     		if(config != null){
-...
     	//TODO: Exception handling
     	/**
+    	 *
     	 * @param state
     	 * @return
     	 */
     	private CsvDemoRecord assembleRecord(CsvDemoExportState state) {
     		if(state!=null){
-...
     		return null;
+    	}
     	/**
     	 * handles the information record for the actual {@link Taxon} including {@link Classification classification}, Taxon Name, Taxon ID,
     	 * Taxon Status, Synonyms, {@link Feature features} data
+    	 *
     	 * @param record the concrete information record
     	 * @param taxonBase {@link Taxon}
     	 * @param name
     	 * @param acceptedTaxon
     	 * @param parent
     	 * @param basionym
     	 * @param isPartial
     	 * @param isProParte
     	 * @param config
     	 * @param node
     	 * @param node
     	 * @param type
     	 */
     	private void handleTaxonBase(CsvDemoRecord record, TaxonBase<?> taxonBase,
     			INonViralName name, Classification classification,
-...
     		if(config.isRedlistFeatures()){
     			if(features!= null) {
     				List<List<String>> featureCells = new ArrayList<List<String>>(features.size());
     				List<List<String>> featureCells = new ArrayList<>(features.size());
     				for(int i = 0; i < features.size(); i++) {
     					featureCells.add(new ArrayList<String>());
     					featureCells.add(new ArrayList<>());
+    				}
     				handleRelatedRedlistStatus(record, taxon, false, featureCells, features);
     				handleRelatedRedlistStatus(record, taxon, true, featureCells, features);
+    			}
+    		}
-...
+    		}
+    	}
     	/**
     	 * @param record
     	 * @param name
     	 * @param type
     	 * @param isPartial
     	 * @param isProParte
     	 */
     	private void handleTaxonomicStatus(
     			CsvDemoRecord record,
     			INonViralName name,
-...
+    	}
     	/**
+    	 *
     	 * This method concatenates several synonyms in a list.
+    	 *
     	 * @param record
     	 * @param taxon
     	 */
     	private void handleSynonyms(CsvDemoRecord record, Taxon taxon) {
-...
     		record.setSynonyms(synonymLabels);
+    	}
     	/**
+    	 *
     	 * @param record
     	 * @param taxon
     	 */
     	private void handleDiscriptionData(CsvDemoRecord record, Taxon taxon) {
     		Set<TaxonDescription> descriptions = taxon.getDescriptions();
-...
+    		}
     		record.setCountryCode(distributions);
+    	}
     	/**
+    	 *
     	 * @param record
     	 * @param taxon
     	 * @param featureCells
     	 * @param features
     	 */
     	private void handleRedlistStatus(CsvDemoRecord record, Taxon taxon, List<List<String>> featureCells, List<Feature> features){
     		Set<TaxonDescription> descriptions = taxon.getDescriptions();
-...
     		record.setFeatures(featureCells);
+    	}
     	/**
+    	 *
     	 * @param record
     	 * @param taxon
     	 * @param relationFrom
     	 * @param featureCells
     	 * @param features
     	 */
     	private void handleRelatedRedlistStatus(CsvDemoRecord record, Taxon taxon, boolean relationFrom, List<List<String>> featureCells, List<Feature> features) {
     		if (relationFrom) {
                 handleRedlistStatus(record, taxon, featureCells, features);
+            }
     		Set<TaxonRelationship> taxRels;
     		if(relationFrom){
     			taxRels = taxon.getRelationsFromThisTaxon();
-...
+    		}
+    	}
     	/**
+    	 *
     	 * @param taxonNodes
     	 */
     	private void sortTaxonNodes(List<TaxonNode> taxonNodes) {
     		Collections.sort(taxonNodes, new Comparator<TaxonNode>() {
-...
     		return ! state.getConfig().isDoTaxa();
+    	}
         /**
          * {@inheritDoc}
          */
         @Override
         public byte[] getByteArray() {
             if (this.exportStream != null){
-...
+            }
             return null;
+        }
+    }
+    }

     import java.util.Set;
     import java.util.UUID;
     import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
     import org.apache.logging.log4j.LogManager;
     import org.apache.logging.log4j.Logger;
     import org.springframework.stereotype.Component;
     import eu.etaxonomy.cdm.common.CdmUtils;
-...
+     *
      * @author a.mueller
      * @since 04.04.2017
+     *
      */
     @Component
     public class ExcelDistributionUpdate
-...
         private static final String AREA_MAP = "AreaMap";
         /**
          * {@inheritDoc}
          */
         @Override
         protected void analyzeRecord(Map<String, String> record, ExcelDistributionUpdateState state) {
             // nothing to do
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         protected void firstPass(ExcelDistributionUpdateState state) {
             Map<String, String> record = state.getOriginalRecord();
-...
+            }
+        }
         /**
          * @param state
          * @param taxon
          * @param record
          * @param line
          */
         private void handleAreasForTaxon(ExcelDistributionUpdateState state, Taxon taxon, Map<String, String> record,
                 String line) {
             ImportResult result = state.getResult();
-...
+            }
+        }
         /**
          * @param taxon
          * @return
          */
         private String getTaxonLabel(Taxon taxon) {
             return taxon.getName() == null ? taxon.getTitleCache() : taxon.getName().getTitleCache();
+        }
-...
             return result;
+        }
         /**
          * @param statusStr
          * @return
          */
         private PresenceAbsenceTerm getStatusByStatusStr(ExcelDistributionUpdateState state, String statusStr, String line) {
     //        FIXME replace hardcoded;
             if ("A".equals(statusStr)) {
-...
             return null;
+        }
         /**
          * @param state
          * @param key
          * @param line
          * @return
          */
         private NamedArea getAreaByIdInVoc(ExcelDistributionUpdateState state, String id, String line) {
             //TODO remember in state
             Map<String, NamedArea> areaMap = (Map<String, NamedArea>)state.getStatusItem(AREA_MAP);
-...
             return area;
+        }
         /**
          * @param state
          * @return
          */
         private Map<String, NamedArea> createAreaMap(ExcelDistributionUpdateState state) {
             Map<String, NamedArea> result = new HashMap<>();
             TermVocabulary<?> voc = getVocabularyService().find(state.getConfig().getAreaVocabularyUuid());
-...
             return result;
+        }
         /**
          * @param keys
          * @return
          */
         private Set<String> removeNonAreaKeys(Set<String> keys) {
             Iterator<String> it = keys.iterator();
             while (it.hasNext()){
-...
             return false;
+        }
         /**
          * @param state
          * @param taxon
          * @param line
          * @return
          */
         private Map<NamedArea, Set<Distribution>> getExistingDistributions(
                 ExcelDistributionUpdateState state, Taxon taxon,
                 String line) {
-...
             return result;
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         protected void secondPass(ExcelDistributionUpdateState state) {
             // nothing to do
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         protected boolean isIgnore(ExcelDistributionUpdateState state) {
             return false;
+        }
         @Override
         protected boolean requiresNomenclaturalCode() {
             return false;
+        }
+    }
+    }

     /**
     * Copyright (C) 2007 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.out;
     import java.io.FileNotFoundException;
     import java.io.IOException;
     import eu.etaxonomy.cdm.common.URI;
     import java.util.List;
     import javax.xml.stream.XMLStreamException;
     import javax.xml.stream.XMLStreamWriter;
     import org.apache.commons.lang.StringUtils;
     import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
     import org.springframework.stereotype.Component;
     import eu.etaxonomy.cdm.io.dwca.out.DwcaMetaDataRecord.FieldEntry;
     /**
      * @author a.mueller
      * @since 20.04.2011
      */
     @Component
     public class DwcaMetaDataExport extends DwcaExportBase {
         private static final long serialVersionUID = -4033439569151252697L;
         private static final Logger logger = LogManager.getLogger(DwcaMetaDataExport.class);
     	protected static final String fileName = "meta.xml";
     	/**
     	 * Constructor
     	 */
     	public DwcaMetaDataExport() {
     		super();
     		this.ioName = this.getClass().getSimpleName();
+    	}
     	/**
     	 * {@inheritDoc}
     	 */
     	@Override
     	protected void doInvoke(DwcaTaxExportState state){
     		DwcaTaxExportConfigurator config = state.getConfig();
     		DwcaMetaDataRecord metaDataRecord = new DwcaMetaDataRecord(! IS_CORE, fileName, null);
     		metaDataRecord.setMetaData(true);
     		state.addMetaRecord(metaDataRecord);
     		XMLStreamWriter writer = null;
     		try {
     			writer = createXmlStreamWriter(state, DwcaTaxExportFile.METADATA);
     			String rootNamespace = "http://rs.tdwg.org/dwc/text/";
     			String rootName = "archive";
     			List<DwcaMetaDataRecord> metaRecords = state.getMetaRecords();
     			// create header
     			writer.writeStartDocument();
     			writer.setDefaultNamespace(rootNamespace);
     				// create root element
     				writer.writeStartElement(rootName);
     				writer.writeNamespace(null, rootNamespace);
     				writer.writeNamespace("xsi", "http://www.w3.org/2001/XMLSchema-instance");
     				writer.writeAttribute("http://www.w3.org/2001/XMLSchema-instance", "schemaLocation", "http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd");
     				for (DwcaMetaDataRecord metaRecord : metaRecords){
     					if (! metaRecord.isMetaData()){
     						writeMetaDataRecord(writer, config, metaRecord);
+    					}
+    				}
     				writer.writeEndElement();
     			writer.writeEndDocument();
     			writer.flush();
     			writer.close();
     		} catch (FileNotFoundException e) {
     		    String message = "Metadata file could not be found";
     			state.getResult().addException(e, message);
     		} catch (XMLStreamException e) {
     			if (e.getNestedException() != null){
     			    String message = "Nested XMLStreamException while handling metadata";
     			    state.getResult().addException((Exception)e.getNestedException(), message);
     			}else{
     			    String message = "XMLStreamException while handling metadata";
                     state.getResult().addException(e, message);
+    			}
     		} catch (IOException e) {
     		    String message = "IOException while handling metadata";
                 state.getResult().addException(e, message);
     		} finally{
     			closeWriter(writer, state);
+    		}
     		return;
+    	}
     	private void writeMetaDataRecord(XMLStreamWriter writer,
     			DwcaTaxExportConfigurator config, DwcaMetaDataRecord metaRecord) throws XMLStreamException {
     		if (! metaRecord.hasEntries()){
     			return;
+    		}
     		String encoding = config.getEncoding();
     		String linesTerminatedBy = config.getLinesTerminatedBy();
     		String fieldsEnclosedBy = config.getFieldsEnclosedBy();
     		String ignoreHeaderLines = config.isHasHeaderLines()? "1":"0";
     		String fieldsTerminatedBy= config.getFieldsTerminatedBy();
     		// create core element
     		String elementName = metaRecord.isCore()? "core": "extension";
     		String rowType = metaRecord.getRowType();
     		writeElementStart(writer, elementName, encoding, linesTerminatedBy,	fieldsEnclosedBy,
     		        fieldsTerminatedBy, ignoreHeaderLines, rowType);
     			String filename = metaRecord.getFileLocation();
     			writeFiles(writer, filename );
     			writeId(writer, metaRecord.isCore());
     			List<FieldEntry> entryList = metaRecord.getEntries();
     			for (FieldEntry fieldEntry : entryList){
     				if (fieldEntry.index != 0){
     					writeFieldLine(writer, fieldEntry.index, fieldEntry.term, fieldEntry.defaultValue);
+    				}
+    			}
     		writer.writeEndElement();
+    	}
     	private void writeFieldLine(XMLStreamWriter writer, int index, URI term, String defaultValue) throws XMLStreamException {
     		writer.writeStartElement("field");
     		if (StringUtils.isNotBlank(defaultValue)){
     			writer.writeAttribute("default", defaultValue);
     		}else{
     			writer.writeAttribute("index", String.valueOf(index));
+    		}
     		writer.writeAttribute("term", term.toString());
     		writer.writeEndElement();
+    	}
     	private void writeId(XMLStreamWriter writer, boolean isCore) throws XMLStreamException {
     		String strId = isCore? "id" : "coreid";
     		writer.writeStartElement(strId);
     		writer.writeAttribute("index", "0");
     		writer.writeEndElement();
+    	}
     	private void writeFiles(XMLStreamWriter writer, String filename) throws XMLStreamException {
     		writer.writeStartElement("files");
     			writer.writeStartElement("location");
     			writer.writeCharacters(filename);
     			writer.writeEndElement();
     		writer.writeEndElement();
+    	}
     	/**
     	 * @param writer
     	 * @param encoding
     	 * @param linesTerminatedBy
     	 * @param fieldsEnclosedBy
     	 * @param ignoreHeaderLines
     	 * @param rowType
     	 * @param elementName
     	 * @throws XMLStreamException
     	 */
     	private void writeElementStart(XMLStreamWriter writer, String elementName, String encoding,
     			String linesTerminatedBy, String fieldsEnclosedBy, String fieldsTerminatedBy,
     			String ignoreHeaderLines, String rowType)
     			throws XMLStreamException {
     		writer.writeStartElement(elementName);
     		writer.writeAttribute( "encoding", encoding );
     		writer.writeAttribute( "linesTerminatedBy", linesTerminatedBy );
     		writer.writeAttribute( "fieldsEnclosedBy", fieldsEnclosedBy );
     		writer.writeAttribute("fieldsTerminatedBy", fieldsTerminatedBy);
     		writer.writeAttribute("ignoreHeaderLines", ignoreHeaderLines);
     		writer.writeAttribute("rowType", rowType);
+    	}
     	@Override
     	protected boolean doCheck(DwcaTaxExportState state) {
     		boolean result = true;
     		logger.warn("No check implemented for " + this.ioName);
     		return result;
+    	}
     	@Override
     	protected boolean isIgnore(DwcaTaxExportState state) {
     		return ! state.getConfig().isDoMetaData();
+    	}
+    }
     /**
     * Copyright (C) 2007 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.out;
     import java.io.FileNotFoundException;
     import java.io.IOException;
     import java.util.List;
     import javax.xml.stream.XMLStreamException;
     import javax.xml.stream.XMLStreamWriter;
     import org.apache.commons.lang.StringUtils;
     import org.apache.logging.log4j.LogManager;
     import org.apache.logging.log4j.Logger;
     import org.springframework.stereotype.Component;
     import eu.etaxonomy.cdm.common.URI;
     import eu.etaxonomy.cdm.io.dwca.out.DwcaMetaDataRecord.FieldEntry;
     /**
      * @author a.mueller
      * @since 20.04.2011
      */
     @Component
     public class DwcaMetaDataExport extends DwcaExportBase {
         private static final long serialVersionUID = -4033439569151252697L;
         private static final Logger logger = LogManager.getLogger(DwcaMetaDataExport.class);
     	protected static final String fileName = "meta.xml";
     	/**
     	 * Constructor
     	 */
     	public DwcaMetaDataExport() {
     		super();
     		this.ioName = this.getClass().getSimpleName();
+    	}
     	@Override
     	protected void doInvoke(DwcaTaxExportState state){
     		DwcaTaxExportConfigurator config = state.getConfig();
     		DwcaMetaDataRecord metaDataRecord = new DwcaMetaDataRecord(! IS_CORE, fileName, null);
     		metaDataRecord.setMetaData(true);
     		state.addMetaRecord(metaDataRecord);
     		XMLStreamWriter writer = null;
     		try {
     			writer = createXmlStreamWriter(state, DwcaTaxExportFile.METADATA);
     			String rootNamespace = "http://rs.tdwg.org/dwc/text/";
     			String rootName = "archive";
     			List<DwcaMetaDataRecord> metaRecords = state.getMetaRecords();
     			// create header
     			writer.writeStartDocument();
     			writer.setDefaultNamespace(rootNamespace);
     				// create root element
     				writer.writeStartElement(rootName);
     				writer.writeNamespace(null, rootNamespace);
     				writer.writeNamespace("xsi", "http://www.w3.org/2001/XMLSchema-instance");
     				writer.writeAttribute("http://www.w3.org/2001/XMLSchema-instance", "schemaLocation", "http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd");
     				for (DwcaMetaDataRecord metaRecord : metaRecords){
     					if (! metaRecord.isMetaData()){
     						writeMetaDataRecord(writer, config, metaRecord);
+    					}
+    				}
     				writer.writeEndElement();
     			writer.writeEndDocument();
     			writer.flush();
     			writer.close();
     		} catch (FileNotFoundException e) {
     		    String message = "Metadata file could not be found";
     			state.getResult().addException(e, message);
     		} catch (XMLStreamException e) {
     			if (e.getNestedException() != null){
     			    String message = "Nested XMLStreamException while handling metadata";
     			    state.getResult().addException((Exception)e.getNestedException(), message);
     			}else{
     			    String message = "XMLStreamException while handling metadata";
                     state.getResult().addException(e, message);
+    			}
     		} catch (IOException e) {
     		    String message = "IOException while handling metadata";
                 state.getResult().addException(e, message);
     		} finally{
     			closeWriter(writer, state);
+    		}
     		return;
+    	}
     	private void writeMetaDataRecord(XMLStreamWriter writer,
     			DwcaTaxExportConfigurator config, DwcaMetaDataRecord metaRecord) throws XMLStreamException {
     		if (! metaRecord.hasEntries()){
     			return;
+    		}
     		String encoding = config.getEncoding();
     		String linesTerminatedBy = config.getLinesTerminatedBy();
     		String fieldsEnclosedBy = config.getFieldsEnclosedBy();
     		String ignoreHeaderLines = config.isHasHeaderLines()? "1":"0";
     		String fieldsTerminatedBy= config.getFieldsTerminatedBy();
     		// create core element
     		String elementName = metaRecord.isCore()? "core": "extension";
     		String rowType = metaRecord.getRowType();
     		writeElementStart(writer, elementName, encoding, linesTerminatedBy,	fieldsEnclosedBy,
     		        fieldsTerminatedBy, ignoreHeaderLines, rowType);
     			String filename = metaRecord.getFileLocation();
     			writeFiles(writer, filename );
     			writeId(writer, metaRecord.isCore());
     			List<FieldEntry> entryList = metaRecord.getEntries();
     			for (FieldEntry fieldEntry : entryList){
     				if (fieldEntry.index != 0){
     					writeFieldLine(writer, fieldEntry.index, fieldEntry.term, fieldEntry.defaultValue);
+    				}
+    			}
     		writer.writeEndElement();
+    	}
     	private void writeFieldLine(XMLStreamWriter writer, int index, URI term, String defaultValue) throws XMLStreamException {
     		writer.writeStartElement("field");
     		if (StringUtils.isNotBlank(defaultValue)){
     			writer.writeAttribute("default", defaultValue);
     		}else{
     			writer.writeAttribute("index", String.valueOf(index));
+    		}
     		writer.writeAttribute("term", term.toString());
     		writer.writeEndElement();
+    	}
     	private void writeId(XMLStreamWriter writer, boolean isCore) throws XMLStreamException {
     		String strId = isCore? "id" : "coreid";
     		writer.writeStartElement(strId);
     		writer.writeAttribute("index", "0");
     		writer.writeEndElement();
+    	}
     	private void writeFiles(XMLStreamWriter writer, String filename) throws XMLStreamException {
     		writer.writeStartElement("files");
     			writer.writeStartElement("location");
     			writer.writeCharacters(filename);
     			writer.writeEndElement();
     		writer.writeEndElement();
+    	}
     	/**
     	 * @param writer
     	 * @param encoding
     	 * @param linesTerminatedBy
     	 * @param fieldsEnclosedBy
     	 * @param ignoreHeaderLines
     	 * @param rowType
     	 * @param elementName
     	 * @throws XMLStreamException
     	 */
     	private void writeElementStart(XMLStreamWriter writer, String elementName, String encoding,
     			String linesTerminatedBy, String fieldsEnclosedBy, String fieldsTerminatedBy,
     			String ignoreHeaderLines, String rowType)
     			throws XMLStreamException {
     		writer.writeStartElement(elementName);
     		writer.writeAttribute( "encoding", encoding );
     		writer.writeAttribute( "linesTerminatedBy", linesTerminatedBy );
     		writer.writeAttribute( "fieldsEnclosedBy", fieldsEnclosedBy );
     		writer.writeAttribute("fieldsTerminatedBy", fieldsTerminatedBy);
     		writer.writeAttribute("ignoreHeaderLines", ignoreHeaderLines);
     		writer.writeAttribute("rowType", rowType);
+    	}
     	@Override
     	protected boolean doCheck(DwcaTaxExportState state) {
     		boolean result = true;
     		logger.warn("No check implemented for " + this.ioName);
     		return result;
+    	}
     	@Override
     	protected boolean isIgnore(DwcaTaxExportState state) {
     		return ! state.getConfig().isDoMetaData();
+    	}
+    }

     import java.io.IOException;
     import java.io.PrintWriter;
     import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
     import org.apache.logging.log4j.LogManager;
     import org.apache.logging.log4j.Logger;
     import org.springframework.stereotype.Component;
     /**
-...
+     *
      * @author a.mueller
      * @since 25.06.2017
+     *
      */
     @Component
     public class DwcaResultWriter extends DwcaExportBase {
-...
         @SuppressWarnings("unused")
         private static final Logger logger = LogManager.getLogger(DwcaDescriptionExport.class);
         /**
          * {@inheritDoc}
          */
         @Override
         protected void doInvoke(DwcaTaxExportState state) {
             addReport(state);
-...
+            }
+        }
         /**
          * @param state
          */
         protected void closeZip(DwcaTaxExportState state) {
             if (state.isZip()){
                 try {
-...
+            }
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         protected boolean doCheck(DwcaTaxExportState state) {
             return false;
+        }
         /**
          * {@inheritDoc}
          */
         @Override
         protected boolean isIgnore(DwcaTaxExportState state) {
             return false;
+        }
+    }
+    }

     /**
     * Copyright (C) 2007 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.out;
     import java.io.FileNotFoundException;
     import java.io.IOException;
     import java.io.UnsupportedEncodingException;
     import java.util.Arrays;
     import java.util.List;
     import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
     import org.springframework.beans.factory.annotation.Autowired;
     import org.springframework.stereotype.Component;
     import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
     import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
     import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
     import eu.etaxonomy.cdm.io.common.TaxonNodeOutStreamPartitioner;
     import eu.etaxonomy.cdm.io.common.XmlExportState;
     import eu.etaxonomy.cdm.model.taxon.TaxonNode;
     /**
      * @author a.mueller
      * @since 18.04.2011
      */
     @Component
     public class DwcaTaxExport extends DwcaExportBase {
         private static final long serialVersionUID = -3770976064909193441L;
         private static final Logger logger = LogManager.getLogger(DwcaTaxExport.class);
         @Autowired
         private ITaxonNodeService taxonNodeService;
     	public DwcaTaxExport() {
     		super();
     		this.ioName = this.getClass().getSimpleName();
             file = DwcaTaxExportFile.TAXON;
+    	}
         /**
          * {@inheritDoc}
          */
         @Override
         public long countSteps(DwcaTaxExportState state) {
             TaxonNodeFilter filter = state.getConfig().getTaxonNodeFilter();
             return taxonNodeService.count(filter);
+        }
     	/**
     	 * Retrieves data from a CDM DB and serializes the CDM to XML.
     	 * Starts with root taxa and traverses the classification to retrieve children taxa, synonyms and relationships.
     	 * Taxa that are not part of the classification are not found.
     	 * <BR>
     	 * {@inheritDoc}
     	 */
     	@Override
     	protected void doInvoke(DwcaTaxExportState state){
     	    IProgressMonitor monitor = state.getConfig().getProgressMonitor();
     		List<DwcaDataExportBase> exports =  Arrays.asList(new DwcaDataExportBase[]{
     	        new DwcaTaxonExport(state),
     	        new DwcaReferenceExport(state),
     	        new DwcaResourceRelationExport(state),
     	        new DwcaTypesExport(state),
     	        new DwcaVernacularExport(state),
     	        new DwcaDescriptionExport(state),
     	        new DwcaDistributionExport(state),
     	        new DwcaImageExport(state)
     		});
     		@SuppressWarnings("unchecked")
     	    TaxonNodeOutStreamPartitioner<XmlExportState> partitioner
     	          = TaxonNodeOutStreamPartitioner.NewInstance(
                         this, state, state.getConfig().getTaxonNodeFilter(),
 , monitor, null);
     		try {
     		    monitor.subTask("Start partitioning");
     		    TaxonNode node = partitioner.next();
     			while (node != null){
     			    for (DwcaDataExportBase export : exports){
     			        handleTaxonNode(export, state, node);
+    			    }
     			    node = partitioner.next();
+    			}
     		} catch (Exception e) {
     		    String message = "Unexpected exception: " + e.getMessage();
     			state.getResult().addException(e, message, "DwcaTaxExport.doInvoke()");
+    		}
     		finally{
     		    if(partitioner != null){
     		        partitioner.close();
+    		    }
     		    for (DwcaDataExportBase export : exports){
     		        closeWriter(export, state);
+                }
+    		}
     		return;
+    	}
         /**
          * @param taxonExport
          * @param state
          */
         private void closeWriter(DwcaDataExportBase export, DwcaTaxExportState state) {
             if (!export.isIgnore(state)){
                 export.closeWriter(state);
+            }
+        }
         private void handleTaxonNode(DwcaDataExportBase export, DwcaTaxExportState state, TaxonNode node) throws FileNotFoundException, UnsupportedEncodingException, IOException {
             if (!export.isIgnore(state)){
                 export.handleTaxonNode(state, node);
+            }
+        }
     	@Override
     	protected boolean doCheck(DwcaTaxExportState state) {
     		boolean result = true;
     		logger.warn("No check implemented for " + this.ioName);
     		return result;
+    	}
     	@Override
     	public boolean isIgnore(DwcaTaxExportState state) {
     		return ! state.getConfig().isDoTaxa();
+    	}
+    }
     /**
     * Copyright (C) 2007 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.out;
     import java.io.FileNotFoundException;
     import java.io.IOException;
     import java.io.UnsupportedEncodingException;
     import java.util.Arrays;
     import java.util.List;
     import org.apache.logging.log4j.LogManager;
     import org.apache.logging.log4j.Logger;
     import org.springframework.beans.factory.annotation.Autowired;
     import org.springframework.stereotype.Component;
     import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
     import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
     import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
     import eu.etaxonomy.cdm.io.common.TaxonNodeOutStreamPartitioner;
     import eu.etaxonomy.cdm.io.common.XmlExportState;
     import eu.etaxonomy.cdm.model.taxon.TaxonNode;
     /**
      * @author a.mueller
      * @since 18.04.2011
      */
     @Component
     public class DwcaTaxExport extends DwcaExportBase {
         private static final long serialVersionUID = -3770976064909193441L;
         private static final Logger logger = LogManager.getLogger(DwcaTaxExport.class);
         @Autowired
         private ITaxonNodeService taxonNodeService;
     	public DwcaTaxExport() {
     		super();
     		this.ioName = this.getClass().getSimpleName();
             file = DwcaTaxExportFile.TAXON;
+    	}
         @Override
         public long countSteps(DwcaTaxExportState state) {
             TaxonNodeFilter filter = state.getConfig().getTaxonNodeFilter();
             return taxonNodeService.count(filter);
+        }
     	/**
     	 * Retrieves data from a CDM DB and serializes the CDM to XML.
     	 * Starts with root taxa and traverses the classification to retrieve children taxa, synonyms and relationships.
     	 * Taxa that are not part of the classification are not found.
     	 * <BR>
     	 * {@inheritDoc}
     	 */
     	@Override
     	protected void doInvoke(DwcaTaxExportState state){
     	    IProgressMonitor monitor = state.getConfig().getProgressMonitor();
     		List<DwcaDataExportBase> exports =  Arrays.asList(new DwcaDataExportBase[]{
     	        new DwcaTaxonExport(state),
     	        new DwcaReferenceExport(state),
     	        new DwcaResourceRelationExport(state),
     	        new DwcaTypesExport(state),
     	        new DwcaVernacularExport(state),
     	        new DwcaDescriptionExport(state),
     	        new DwcaDistributionExport(state),
     	        new DwcaImageExport(state)
     		});
     		@SuppressWarnings("unchecked")
     	    TaxonNodeOutStreamPartitioner<XmlExportState> partitioner
     	          = TaxonNodeOutStreamPartitioner.NewInstance(
                         this, state, state.getConfig().getTaxonNodeFilter(),
 , monitor, null);
     		try {
     		    monitor.subTask("Start partitioning");
     		    TaxonNode node = partitioner.next();
     			while (node != null){
     			    for (DwcaDataExportBase export : exports){
     			        handleTaxonNode(export, state, node);
+    			    }
     			    node = partitioner.next();
+    			}
     		} catch (Exception e) {
     		    String message = "Unexpected exception: " + e.getMessage();
     			state.getResult().addException(e, message, "DwcaTaxExport.doInvoke()");
+    		}
     		finally{
     		    if(partitioner != null){
     		        partitioner.close();
+    		    }
     		    for (DwcaDataExportBase export : exports){
     		        closeWriter(export, state);
+                }
+    		}
     		return;
+    	}
         /**
          * @param taxonExport
          * @param state
          */
         private void closeWriter(DwcaDataExportBase export, DwcaTaxExportState state) {
             if (!export.isIgnore(state)){
                 export.closeWriter(state);
+            }
+        }
         private void handleTaxonNode(DwcaDataExportBase export, DwcaTaxExportState state, TaxonNode node) throws FileNotFoundException, UnsupportedEncodingException, IOException {
             if (!export.isIgnore(state)){
                 export.handleTaxonNode(state, node);
+            }
+        }
     	@Override
     	protected boolean doCheck(DwcaTaxExportState state) {
     		boolean result = true;
     		logger.warn("No check implemented for " + this.ioName);
     		return result;
+    	}
     	@Override
     	public boolean isIgnore(DwcaTaxExportState state) {
     		return ! state.getConfig().isDoTaxa();
+    	}
+    }

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Revision f104a204

Added by Andreas Müller almost 2 years ago