/ - Diff - EDIT - EDIT Project Management

     * 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.common.mapping;
     import java.sql.ResultSet;
-...
     import org.apache.commons.lang3.StringUtils;
     import org.apache.log4j.Logger;
     /**
      * @author a.mueller
      * @since 12.05.2009
      * @version 1.0
      */
     public abstract class MultipleAttributeMapperBase<SINGLE_MAPPER extends CdmSingleAttributeMapperBase> extends CdmAttributeMapperBase {
     	@SuppressWarnings("unused")
-...
     //******************************* ATTRIBUTES ***************************************/
     	protected List<SINGLE_MAPPER> singleMappers = new ArrayList<SINGLE_MAPPER>();
     	protected List<SINGLE_MAPPER> singleMappers = new ArrayList<>();
     //********************************* CONSTRUCTOR ****************************************/
     	/**
+    	 *
     	 */
     	public MultipleAttributeMapperBase() {
     		singleMappers = new ArrayList<SINGLE_MAPPER>();
+    	}
     //************************************ METHODS *******************************************/
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.io.common.CdmAttributeMapperBase#getDestinationAttributeList()
     	 */
     	@Override
     	public List<String> getDestinationAttributeList() {
     		List<String> result = new ArrayList<String>();
     		List<String> result = new ArrayList<>();
     		for (SINGLE_MAPPER singleMapper : singleMappers){
     			result.addAll(singleMapper.getDestinationAttributeList());
+    		}
     		return result;
+    	}
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.io.common.CdmAttributeMapperBase#getDestinationAttributes()
     	 */
     	@Override
     	public Set<String> getDestinationAttributes() {
     		Set<String> result = new HashSet<String>();
     		Set<String> result = new HashSet<>();
     		result.addAll(getDestinationAttributeList());
     		return result;
+    	}
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.io.common.CdmAttributeMapperBase#getSourceAttributeList()
     	 */
     	@Override
     	public List<String> getSourceAttributeList() {
     		List<String> result = new ArrayList<String>();
     		List<String> result = new ArrayList<>();
     		for (SINGLE_MAPPER singleMapper : singleMappers){
     			result.addAll(singleMapper.getSourceAttributeList());
+    		}
     		return result;
+    	}
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.io.common.CdmAttributeMapperBase#getSourceAttributes()
     	 */
     	@Override
     	public Set<String> getSourceAttributes() {
     		Set<String> result = new HashSet<String>();
     		Set<String> result = new HashSet<>();
     		result.addAll(getSourceAttributeList());
     		return result;
+    	}
     /**
         /**
     	 * Returns the value of a result set attribute in its String representation.
     	 * Better move this to a subclass for DbImportMappers (does not exist yet)
     	 */

     /**
     * Copyright (C) 2007 EDIT
     * European Distributed Institute of Taxonomy
     * 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.
     */
-...
     		this.oneClass = oneClass;
     		this.singleAttributeName = singleAttributeName;
+    	}
     //	@Override
     //	public Set<String> getSourceAttributes(){
     //		Set<String> result = new HashSet<String>();
     //		Set<String> result = new HashSet<>();
     //		result.addAll(getSourceAttributeList());
     //		return result;
     //	}
     	@Override
     	public List<String> getSourceAttributeList(){
     		List<String> result = new ArrayList<String>();
-...
+    		}
     		return result;
+    	}
     //	@Override
     //	public Set<String> getDestinationAttributes(){
     //		Set<String> result = new HashSet<String>();
     //		Set<String> result = new HashSet<>();
     //		result.addAll(getDestinationAttributeList());
     //		return result;
     //	}
     	@Override
     	public List<String> getDestinationAttributeList(){
     		List<String> result = new ArrayList<String>();
-...
     		return result;
+    	}
     	public Class<MANY> getManyClass(){
     		return manyClass;
+    	}
     	public Class<ONE> getOneClass(){
     		return oneClass;
+    	}
     	public String getDestinationAttribute(String sourceAttribute){
     		if (sourceAttribute == null){
     			return null;
-...
+    		}
     		return null;
+    	}
     	public List<SINGLE_MAPPER> getSingleMappers(){
     		return singleMappers;
+    	}
-...
     	public String getSingleAttributeName() {
     		return singleAttributeName;
+    	}
+    }

     	@Override
     	public Set<String> getSourceAttributes() {
     		Set<String> result = new HashSet<String>();
     		Set<String> result = new HashSet<>();
     		if (cdmAttribute != null){
     			result.add(cdmAttribute);
+    		}

cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/DwcTaxonCsv2CdmTaxonRelationConverter.java
52	52
53	53	private static final String ID = "id";
54	54
55		/**
56		* @param state
57		*/
58	55	public DwcTaxonCsv2CdmTaxonRelationConverter(DwcaDataImportStateBase state) {
59	56	super(state);
60	57	}
...	...
68	65	}
69	66	}
70	67
71
72	68	@Override
73	69	public IReader<MappedCdmBase<? extends CdmBase>> map(StreamItem item){
74	70	List<MappedCdmBase<? extends CdmBase>> resultList = new ArrayList<>();
...	...
137	133	return new ListReader<>(resultList);
138	134	}
139	135
140
141	136	@Override
142	137	public String getSourceId(StreamItem item) {
143	138	String id = item.get(ID);
144	139	return id;
145	140	}
146	141
147
148	142	private void handleSubGenus(StreamItem item, DwcaDataImportStateBase<DwcaDataImportConfiguratorBase> state) {
149	143	// TODO Auto-generated method stub
150	144	}
...	...
173	167	// TODO Auto-generated method stub
174	168	}
175	169
176
177	170	private void handleParentNameUsage(StreamItem item, DwcaDataImportStateBase<DwcaDataImportConfiguratorBase> state,
178	171	TaxonBase<?> taxonBase, String id, List<MappedCdmBase<? extends CdmBase>> resultList) {
179	172
...	...
222	215	}
223	216	}
224	217
225
226	218	private Classification getClassification(StreamItem item, List<MappedCdmBase<? extends CdmBase>> resultList) {
227	219	Set<Classification> resultSet = new HashSet<>();
228	220	//
...	...
260	252	return resultSet.iterator().next();
261	253	}
262	254
263
264	255	private void handleAcceptedNameUsage(StreamItem item, DwcaDataImportStateBase<DwcaDataImportConfiguratorBase> state, TaxonBase<?> taxonBase, String id) {
265	256	if (acceptedNameUsageExists(item)){
266	257	String accId = item.get(TermUri.DWC_ACCEPTED_NAME_USAGE_ID);
...	...
270	261	}
271	262	}
272	263
273
274		/**
275		* @param item
276		* @param state
277		* @param taxonBase
278		* @param id
279		* @param accId
280		* @param taxStatus
281		*/
282	264	private void handleAcceptedNameUsageParam(StreamItem item,
283	265	DwcaDataImportStateBase<DwcaDataImportConfiguratorBase> state, TaxonBase<?> taxonBase, String id, String accId) {
284	266	if (id.equals(accId)){
...	...
313	295	}
314	296	}
315	297
316
317		/**
318		* @param item
319		* @return
320		*/
321	298	private boolean acceptedNameUsageExists(StreamItem item) {
322	299	return exists(TermUri.DWC_ACCEPTED_NAME_USAGE_ID, item) \|\| exists(TermUri.DWC_ACCEPTED_NAME_USAGE, item);
323	300	}
324	301
325
326
327	302	//************************** PARTITIONABLE **********************************************
328	303
329	304	@Override
...	...
381	356
382	357	@Override
383	358	public Set<String> requiredSourceNamespaces() {
384		Set<String> result = new HashSet<String>();
	359	Set<String> result = new HashSet<>();
385	360
386	361	result.add(TermUri.DWC_TAXON.toString());
387	362
...	...
400	375	return result;
401	376	}
402	377
403
404	378	//*********************************** TO STRING ******************************************
405	379
406	380	@Override
407	381	public String toString(){
408	382	return this.getClass().getName();
409	383	}
410
411
412
413	384	}

     /**
      * @author a.mueller
      * @since 22.11.2011
+     *
      */
     public class GbifDescriptionCsv2CdmConverter extends PartitionableConverterBase<DwcaDataImportConfiguratorBase, DwcaDataImportStateBase<DwcaDataImportConfiguratorBase>>
     						implements IPartitionableConverter<StreamItem, IReader<CdmBase>, String>{
-...
     	private static final String CORE_ID = "coreId";
     	/**
     	 * @param state
     	 */
     	public GbifDescriptionCsv2CdmConverter(DwcaDataImportStateBase state) {
     		super(state);
+    	}
-...
     		return new ListReader<>(resultList);
+    	}
     	/**
     	 * Determines the feature by the dc:type attribute. Tries to reuse existing
     	 * features.
+    	 *
     	 * @param item
     	 * @param resultList
     	 * @return
-...
     			fireWarningEvent(message, item, 8);
     			return null;
+    		}
+    	}
     	@Override
-...
     		return id;
+    	}
     //********************** PARTITIONABLE **************************************/
     	@Override
-...
+    		}
+    	}
     	@Override
     	public Set<String> requiredSourceNamespaces() {
     		Set<String> result = new HashSet<String>();
     		Set<String> result = new HashSet<>();
      		result.add(TermUri.DWC_TAXON.toString());
      		result.add(TermUri.DC_LANGUAGE.toString());
             return result;
-...
     	public String toString(){
     		return this.getClass().getName();
+    	}
+    }

cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/GbifReferenceCsv2CdmConverter.java
49	49	/**
50	50	* @author a.mueller
51	51	* @since 22.11.2011
52		*
53	52	*/
54	53	public class GbifReferenceCsv2CdmConverter extends PartitionableConverterBase<DwcaDataImportConfiguratorBase, DwcaDataImportStateBase<DwcaDataImportConfiguratorBase>>
55	54	implements IPartitionableConverter<StreamItem, IReader<CdmBase>, String>{
...	...
58	57
59	58	private static final String CORE_ID = "coreId";
60	59
61		/**
62		* @param state
63		*/
64	60	public GbifReferenceCsv2CdmConverter(DwcaDataImportStateBase state) {
65	61	super(state);
66	62	}
...	...
112	108	//type
113	109	handleType(reference, strType, taxon, resultList, item);
114	110
115
116	111	return new ListReader<>(resultList);
117	112	}
118	113
119
120	114	private void handleType(Reference reference, String strType, TaxonBase<?> taxon,
121	115	List<MappedCdmBase<? extends CdmBase>> resultList, StreamItem item) {
122	116	// TODO handleType not yet implemented
...	...
166	160	//TODO not yet handled by CDM
167	161	}
168	162	}
169
170	163	}
171	164	}
172	165	if (config.isHandleAllRefsAsCitation()){
...	...
183	176	resultList.add(new MappedCdmBase<CdmBase>(desc));
184	177	}
185	178	}
186
187	179	}
188
189	180	}
190
191
192	181	}
193	182
194	183	private void createCitation(TaxonDescription desc, Reference ref, TaxonName nameUsedInSource) {
...	...
219	208	logger.debug("Reference is not an URI");
220	209	}
221	210	//TODO further identifier types
222
223	211	}
224	212
225	213	private Reference handleInRef(String strSource) {
...	...
231	219	}
232	220	}
233	221
234
235	222	private VerbatimTimePeriod handleDate(String strDate) {
236	223	VerbatimTimePeriod tp = TimePeriodParser.parseStringVerbatim(strDate);
237	224	return tp;
...	...
248	235	return id;
249	236	}
250	237
251
252	238	//******************** PARTITIONABLE ************************************/
253	239
254	240	@Override
...	...
262	248	}
263	249	}
264	250
265
266	251	@Override
267	252	public Set<String> requiredSourceNamespaces() {
268		Set<String> result = new HashSet<String>();
	253	Set<String> result = new HashSet<>();
269	254	result.add(TermUri.DWC_TAXON.toString());
270	255	return result;
271	256	}
...	...
276	261	public String toString(){
277	262	return this.getClass().getName();
278	263	}
279
280
281	264	}

     * 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.excel.taxa;
     import java.util.HashMap;
-...
     	private static final Logger logger = Logger.getLogger(TaxonExcelImportState.class);
         /** Already processed authors */
     	private Set<String> authors = new HashSet<String>();
     	private Set<String> authors = new HashSet<>();
     	private Map<String, TaxonBase> taxonMap= new HashMap<String, TaxonBase>();
     	/**
-...
     	private Taxon parent;
     	private Classification classification;
     	public TaxonExcelImportState(ExcelImportConfiguratorBase config) {
     		super(config);
+    	}
     	/**
     	 * @return the author
     	 */
     	public Set<String> getAuthors() {
     		return authors;
+    	}
     	/**
     	 * @param author the author to set
     	 */
     	public void setAuthors(Set<String> authors) {
     		this.authors = authors;
+    	}
-...
     	public Taxon getParent(){
     	    return parent;
+    	}
     	public void setParent(Taxon parent){
     	    this.parent = parent;
+        }
     	/**
     	 * @param parentId
     	 * @return
     	 */
     	public TaxonBase getTaxonBase(String taxonId) {
     		return taxonMap.get(taxonId);
+    	}
     	/**
     	 * @param parentId
     	 * @param taxon
     	 */
     	public void putTaxon(String taxonId, TaxonBase taxonBase) {
     	    taxonMap.put(taxonId, taxonBase);
+    	}
         /**
          * @return the classification
          */
         public Classification getClassification() {
             return classification;
+        }
         /**
          * @param classification the classification to set
          */
         public void setClassification(Classification classification) {
             this.classification = classification;
+        }
-...
             this.nameMap = nameMap;
+        }
         /**
          * @param name
          * @param name2
          */
         public void putName(String titleCache, TaxonName name) {
             if (nameMap == null){
                 nameMap = new HashMap<String, TaxonName>();
                 nameMap = new HashMap<>();
+            }
             nameMap.put(titleCache, name);
+        }
+    }

     /**
+     *
+     *
      */
     package eu.etaxonomy.cdm.io.markup;
-...
     /**
      * This class is supposed to find the best sorting order for features (descriptive and other).
      * Currently it is not yet very sophisticated.
+     *
      * @author a.mueller
+     *
      * @author a.mueller
      */
     public class FeatureSorter {
     	class FeatureStatistic{
     		private UUID uuid;
-...
     		private int before = 0;   //number of features before this feature
     		private int after = 0;    //number of features after this feature
     		private int n = 0;      //number of occurrences of this feature
     		public FeatureStatistic(UUID uuid) {
     			this.uuid = uuid;
+    		}
-...
     		public String toString(){
     			return uuid != null? uuid.toString(): super.toString();
+    		}
+    	}
     	/**
     	 * Compute the order of features.
     	 * @param orderLists
-...
     	private void removeEmptyLists(Map<String, List<FeatureSorterInfo>> listMap) {
     		Set<String> keysToRemove = new HashSet<String>();
     		Set<String> keysToRemove = new HashSet<>();
     		for(String key : listMap.keySet()){
     			List<FeatureSorterInfo> list = listMap.get(key);
     			if (list.isEmpty()){
-...
     		for (String key : keysToRemove){
     			listMap.remove(key);
+    		}
+    	}
-...
     	 * @param uuid
     	 */
     	private Map<String, List<FeatureSorterInfo>> removeFromLists(Map<String, List<FeatureSorterInfo>> orderListsMap, UUID uuid) {
     		Map<String, List<FeatureSorterInfo>> childLists = new HashMap<String, List<FeatureSorterInfo>>();
     		Map<String, List<FeatureSorterInfo>> childLists = new HashMap<>();
     		Set<String> keySet = orderListsMap.keySet();
     		Iterator<String> keySetIterator = keySet.iterator();
     		while (keySetIterator.hasNext()){
     			String key = keySetIterator.next();
     			List<FeatureSorterInfo> list = orderListsMap.get(key);
     			List<FeatureSorterInfo> list = orderListsMap.get(key);
     			Iterator<FeatureSorterInfo> it = list.listIterator();
     			while (it.hasNext()){
     				FeatureSorterInfo info = it.next();
-...
     		return childLists;
+    	}
     	private FeatureStatistic findBest(Map<UUID, FeatureStatistic> statisticMap) {
     		FeatureStatistic result;
     		Set<FeatureStatistic> highest = getOnlyHighestFeatures(statisticMap);
-...
     		return result;
+    	}
     	/**
     	 * If no feature is always highest this method can be called to use an alternative criteria
     	 * to find the "highest" feature.
+    	 *
     	 * to find the "highest" feature.
+    	 *
     	 * @param statisticMap
     	 * @return
     	 */
-...
     		return result;
+    	}
     	private Set<FeatureStatistic> getOnlyHighestFeatures(Map<UUID, FeatureStatistic> statisticMap) {
     		 Set<FeatureStatistic> result = new HashSet<FeatureStatistic>();
     		 Set<FeatureStatistic> result = new HashSet<>();
     		 for (FeatureStatistic statistic : statisticMap.values()){
     			 if (statistic.isAlwaysHighest){
     				 result.add(statistic);
-...
     	private Map<UUID, FeatureStatistic> computeStatistic(Map<String,List<FeatureSorterInfo>> orderLists) {
     		Map<UUID, FeatureStatistic> result = new HashMap<UUID, FeatureStatistic>();
     		Map<UUID, FeatureStatistic> result = new HashMap<>();
     		for (String key :  orderLists.keySet()){
     			List<FeatureSorterInfo> list = orderLists.get(key);
     			int n = list.size();
-...
     		return result;
+    	}
     	private FeatureStatistic getFeatureStatistic(FeatureSorterInfo info, Map<UUID, FeatureStatistic> statisticMap) {
     		UUID uuid = info.getUuid();
     		FeatureStatistic result = statisticMap.get(uuid);

     /**
      * @author pkelbert
      * @since 21 juin 2013
+     *
      */
     public class SpecimenUserInteraction implements ItemListener, Serializable {
         private static final long serialVersionUID = 6384263183459028523L;
         @SuppressWarnings("unused")
         private static Logger log = Logger.getLogger(SpecimenUserInteraction.class);
         public Classification askForClassification(Map<String, Classification> classMap){
-...
             return classMap.get(s);
+        }
         /**
          * @return the name for the new Classification
          */
-...
             return s;
+        }
         /**
          * @param refMap
          * @return
          */
         @SuppressWarnings("rawtypes")
         public Reference askForReference(Map<String, Reference> refMap) {
             List<String>  possibilities = new ArrayList<String> (refMap.keySet());
             List<String>  possibilities = new ArrayList<>(refMap.keySet());
             Collections.sort(possibilities);
             if (refMap.keySet().size()>0) {
                 refMap.put("Nothing matches, create a new reference",null);
-...
             return refMap.get(s);
+        }
         /**
          * @param refMap
          * @param iReferenceService
          * @param docSources
          * @return
          */
         @SuppressWarnings("rawtypes")
         public List<OriginalSourceBase<?>> askForSource(Map<String, OriginalSourceBase<?>> refMap, String currentElement, String blabla,
                 IReferenceService iReferenceService, List<String> docSources) {
     //        System.out.println(refMap);
             List<String>  possibilities = new ArrayList<String> (refMap.keySet());
             List<String>  possibilities = new ArrayList<> (refMap.keySet());
             Set<String> all = new HashSet<String>();
             Set<String> all = new HashSet<>();
             all.addAll(possibilities);
             List<String> allList = new ArrayList<String>();
-...
                         sources.add(a);
+                    }
+                }
+            }
             List<OriginalSourceBase<?>> dess = new ArrayList<OriginalSourceBase<?>>();
             List<OriginalSourceBase<?>> dess = new ArrayList<>();
             for (String src:sources){
                 if (refMap.get(src) !=null) {
                     dess.add(refMap.get(src));
-...
             return dess;
+        }
         /**
          * @return
          */
         public String createNewReference() {
             JTextArea textArea = new JTextArea("How should the reference be named ?");
             JScrollPane scrollPane = new JScrollPane(textArea);
-...
             return s;
+        }
         /**
          * @return
          */
         public String createNewSource() {
             JTextArea textArea = new JTextArea("How should the source be named? If there is a citation detail, prefix it with 3 minus signs ('---').");
             JScrollPane scrollPane = new JScrollPane(textArea);
-...
             return s;
+        }
         /**
          * @param descriptions
          */
         public TaxonDescription askForDescriptionGroup(Set<TaxonDescription> descriptions) {
             JTextArea textArea = new JTextArea("One or several description group(s) does already exist for this taxon.");
             JScrollPane scrollPane = new JScrollPane(textArea);
-...
                 for (IdentifiableSource s:sources) {
                     src.add(s.getCitation().getTitleCache());
+                }
                 List<String> srcb = new ArrayList<String>(new HashSet<String>(src));
                 List<String> srcb = new ArrayList<String>(new HashSet<>(src));
                 if (srcb.size()>0) {
                     if(descrMap.containsKey(descCnt+": "+description.getTitleCache()+"("+StringUtils.join(srcb,";")+")")) {
                         descCnt+=1;
-...
                     //            }
+                }
+            }
             List<String>  possibilities = new ArrayList<String> (descrMap.keySet());
             List<String>  possibilities = new ArrayList<>(descrMap.keySet());
             if (possibilities.size()==0) {
                 return null;
+            }
-...
             } else {
                 return null;
+            }
+        }
         /**
          * Look if the same name already exists in the ALL classifications and ask the user to select one or none.
          * @param scientificName
-...
          */
         @SuppressWarnings("rawtypes")
         public Taxon askWhereToFixData(String scientificName, List<TaxonBase> taxonList, Classification classification) {
             Map<String,TaxonNode> classMap = new HashMap<String, TaxonNode>();
             Map<String,TaxonNode> classMap = new HashMap<>();
             boolean sameClassification=false;
             Taxon n = null;
             for (TaxonBase taxonBase: taxonList){
-...
             return taxonFound;
+        }
         List<String> sources = new ArrayList<String>();
         List<String> sources = new ArrayList<>();
         String currentSource = "";
         /* (non-Javadoc)
          * @see java.awt.event.ItemListener#itemStateChanged(java.awt.event.ItemEvent)
          */
         @Override
         public void itemStateChanged(ItemEvent e) {
             JRadioButton cb = (JRadioButton) e.getItem();
-...
                 currentSource="";
+            }
+        }
+    }

      * 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.specimen.excel.in;
     import java.io.FileNotFoundException;
-...
      * @author p.kelbert
      * @since 29.10.2008
      * @since 13 mars 2013
+     *
      */
     @Component
     public class SpecimenSythesysExcelImport  extends CdmImportBase<SpecimenSynthesysExcelImportConfigurator, SpecimenSynthesysExcelImportState>
             implements ICdmIO<SpecimenSynthesysExcelImportState> {
         private static final long serialVersionUID = -1145031415387024364L;
         private static final Logger logger = Logger.getLogger(SpecimenSythesysExcelImport.class);
         protected String fullScientificNameString;
-...
          * return empty string instead of null
          * */
         public class MyHashMap<K,V> extends HashMap<K,V> {
             /**
+             *
              */
             private static final long serialVersionUID = -6230407405666753405L;
             @SuppressWarnings("unchecked")
-...
+                    }
                     getClassificationService().saveOrUpdate(classification);
+                }
+            }
+        }
-...
             identifier = unit.get("identifier");
+        }
         private Institution getInstitution(SpecimenSynthesysExcelImportConfigurator config){
             Institution institution;
             List<Institution> institutions;
-...
             return collection;
+        }
         /*
+         *
          * @param app
          * @param derivedThing
          * @param sec
          */
         private void setTaxonName(SpecimenSynthesysExcelImportConfigurator config){
             TaxonName taxonName = null;
             Taxon taxon = null;
-...
                     taxon = addTaxonNode(taxon, config);
+                }
                 DeterminationEvent determinationEvent = DeterminationEvent.NewInstance();
                 determinationEvent.setTaxon(getTaxonService().find(taxon.getUuid()));
                 determinationEvent.setPreferredFlag(preferredFlag);
-...
                 getOccurrenceService().saveOrUpdate(derivedUnitBase);
+            }
+        }
         /**
          * @param taxon
          * @param taxonName
          * @param config
          * @return
          */
         private Taxon addTaxonNode(Taxon taxon, SpecimenSynthesysExcelImportConfigurator config) {
             if (DEBUG) {
                 logger.info("link taxon to a taxonNode");
-...
+                                }
+                            }
                             if (collteam.size()>0) {
                                 collectorinteams.add(new ArrayList<String>(new HashSet<String>(collteam)));
                                 collectorinteams.add(new ArrayList<String>(new HashSet<>(collteam)));
+                            }
+                        }
                         else
-...
+                }
+            }
             List<String> collectorsU = new ArrayList<String>(new HashSet<String>(collectors));
             List<String> teamsU = new ArrayList<String>(new HashSet<String>(teams));
             List<String> collectorsU = new ArrayList<String>(new HashSet<>(collectors));
             List<String> teamsU = new ArrayList<String>(new HashSet<>(teams));
             //existing teams in DB
             Map<String,Team> titleCacheTeam = new HashMap<String, Team>();
             List<UuidAndTitleCache<Team>> hiberTeam = getAgentService().getTeamUuidAndTitleCache();
             Set<UUID> uuids = new HashSet<UUID>();
             Set<UUID> uuids = new HashSet<>();
             for (UuidAndTitleCache<Team> hibernateT:hiberTeam){
                 uuids.add(hibernateT.getUuid());
+            }
-...
+            }
             Map<String,UUID> teamMap = new HashMap<String, UUID>();
             Map<String,UUID> teamMap = new HashMap<>();
             for (UuidAndTitleCache<Team> uuidt:hiberTeam){
                 teamMap.put(uuidt.getTitleCache(), uuidt.getUuid());
+            }
             //existing persons in DB
             List<UuidAndTitleCache<Person>> hiberPersons = getAgentService().getPersonUuidAndTitleCache();
             Map<String,Person> titleCachePerson = new HashMap<String, Person>();
             Map<String,Person> titleCachePerson = new HashMap<>();
             uuids = new HashSet<UUID>();
             for (UuidAndTitleCache<Person> hibernateP:hiberPersons){
                 uuids.add(hibernateP.getUuid());
-...
                 personMap.put(person.getTitleCache(), person.getUuid());
+            }
             java.util.Collection<AgentBase> personsToAdd = new ArrayList<AgentBase>();
             java.util.Collection<AgentBase> teamsToAdd = new ArrayList<AgentBase>();
             java.util.Collection<AgentBase> personsToAdd = new ArrayList<>();
             java.util.Collection<AgentBase> teamsToAdd = new ArrayList<>();
             for (String collector:collectorsU){
                 Person p = Person.NewInstance();
-...
                 titleCachePerson.put(uuuidPerson.get(u).getTitleCache(),CdmBase.deproxy(uuuidPerson.get(u), Person.class) );
+            }
             Person ptmp ;
             Map <String,Integer>teamdone = new HashMap<String, Integer>();
             for (List<String> collteam: collectorinteams){

     	protected Set<String> getKeySet(String key, Map<String, Set<String>> fkMap) {
     		Set<String> keySet = fkMap.get(key);
     		if (keySet == null){
     			keySet = new HashSet<String>();
     			keySet = new HashSet<>();
     			fkMap.put(key, keySet);
+    		}
     		return keySet;

     import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
     import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
     /**
      * @author pkelbert
      * @since 2 avr. 2013
+     *
      */
     public class TaxonXExtractor {
         protected TaxonXImport importer;
         protected TaxonXImportState state2;
         private final Map<String,String> namesAsked = new HashMap<String, String>();
         private final Map<String,Rank>ranksAsked = new HashMap<String, Rank>();
         private final Map<String,String> namesAsked = new HashMap<>();
         private final Map<String,Rank>ranksAsked = new HashMap<>();
         Logger logger = Logger.getLogger(TaxonXExtractor.class);
-...
             private boolean foundBibref=false;
             private final TaxonXAddSources sourceHandler;
             /**
              * @param sourceHandler
              */
             public ReferenceBuilder(TaxonXAddSources sourceHandler) {
                 this.sourceHandler=sourceHandler;
+            }
             /**
              * @return the foundBibref
              */
             public boolean isFoundBibref() {
                 return foundBibref;
+            }
             /**
              * @param foundBibref the foundBibref to set
              */
             public void setFoundBibref(boolean foundBibref) {
                 this.foundBibref = foundBibref;
+            }
             /**
              * @param ref
              * @param refMods
              */
             public void builReference(String mref, String treatmentMainName, NomenclaturalCode nomenclaturalCode,
                     Taxon acceptedTaxon, Reference refMods) {
                 // System.out.println("builReference "+mref);
-...
                 nbRef++;
+            }
+        }
         public class MySpecimenOrObservation{
-...
             public void setDerivedUnitBase(DerivedUnit derivedUnitBase) {
                 this.derivedUnitBase = derivedUnitBase;
+            }
+        }
         /**
          * @param item
          * @return
          */
         @SuppressWarnings({ "unused", "rawtypes" })
         protected MySpecimenOrObservation extractSpecimenOrObservation(Node specimenObservationNode, DerivedUnit derivedUnitBase,
                 SpecimenOrObservationType defaultAssociation, TaxonName typifiableName) {
-...
             unitsGatheringArea.setParams(null, country, state2.getConfig(), importer.getTermService(), importer.getOccurrenceService(), importer.getVocabularyService());
             //TODO other areas
             if (StringUtils.isNotBlank(stateprov)){
             	Map<String, String> namedAreas = new HashMap<String, String>();
             	Map<String, String> namedAreas = new HashMap<>();
             	namedAreas.put(stateprov, null);
                 unitsGatheringArea.setAreaNames(namedAreas, state2.getConfig(), importer.getTermService(), importer.getVocabularyService());
+            }
-...
             return specimenOrObservation;
+        }
         private SpecimenTypeDesignationStatus getSpecimenTypeDesignationStatusByKey(
                 String key) {
             if (key == null) {
-...
             return derivedUnitFacade;
+        }
         @SuppressWarnings("rawtypes")
         protected Feature makeFeature(SpecimenOrObservationBase unit) {
             if (unit == null){
-...
             return null;
+        }
         protected final static String SPLITTER = ",";
         protected  int askQuestion(String question){
             Scanner scan = new Scanner(System.in);
             logger.info(question);
-...
             return index;
+        }
         /**
          * @param reftype
          * @return
          */
         protected Reference getReferenceWithType(int reftype) {
             Reference ref = null;
             switch (reftype) {
-...
+            }
             return ref;
+        }
         /**
          * @param unitsList
          * @param state
          */
         protected void prepareCollectors(TaxonXImportState state,IAgentService agentService) {
             //        logger.info("PREPARE COLLECTORS");
             List<String> collectors = new ArrayList<String>();
             List<String> collectors = new ArrayList<>();
             String tmp;
             List<String> collectorsU = new ArrayList<String>(new HashSet<String>(collectors));
             List<String> collectorsU = new ArrayList<>(new HashSet<>(collectors));
             Set<UUID> uuids = new HashSet<UUID>();
             //existing persons in DB
             List<UuidAndTitleCache<Person>> hiberPersons = agentService.getPersonUuidAndTitleCache();
             Map<String,Person> titleCachePerson = new HashMap<String, Person>();
             Map<String,Person> titleCachePerson = new HashMap<>();
             uuids = new HashSet<UUID>();
             for (UuidAndTitleCache<Person> hibernateP:hiberPersons){
                 uuids.add(hibernateP.getUuid());
-...
+        }
         protected boolean containsDistinctLetters(String word){
             Set<Character> dl = new HashSet<Character>();
             Set<Character> dl = new HashSet<>();
             for (char a: word.toCharArray()) {
                 dl.add(a);
+            }
-...
+        	}
+        }
         /** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
          */
         protected NomenclaturalStatusType nomStatusString2NomStatus (String nomStatus) throws UnknownCdmTypeException{
-...
+            }
+        }
         //TypeDesignation
         protected  SpecimenTypeDesignationStatus typeStatusId2TypeStatus (int typeStatusId)  throws UnknownCdmTypeException{
             switch (typeStatusId){
-...
+            }
+            }
+        }
+    }
+    }

     * 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.tcsrdf;
     import static eu.etaxonomy.cdm.io.common.ImportHelper.OBLIGATORY;
-...
     	protected static String nsTm = "http://rs.tdwg.org/ontology/voc/Team";
     	protected static String nsTpalm = "http://wp5.e-taxonomy.eu/import/palmae/common";
     	@Override
         protected abstract void doInvoke(TcsRdfImportState state);
     //	/* (non-Javadoc)
     //	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
     //	 */
     //	@Override
     //	protected boolean doInvoke(IImportConfigurator config,
     //			Map<String, MapWrapper<? extends CdmBase>> stores){
-...
     	protected boolean makeStandardMapper(Statement resource, CdmBase ref, Set<String> omitAttributes, CdmSingleAttributeRDFMapperBase[] classMappers){
     		if (omitAttributes == null){
     			omitAttributes = new HashSet<String>();
     			omitAttributes = new HashSet<>();
+    		}
     		boolean result = true;
     		for (CdmSingleAttributeRDFMapperBase mapper : classMappers){
-...
     						break;
+    					}
+    				}
     			}else if (content instanceof Text){
     				//empty Text
     				if (((Text)content).getTextNormalize().equals("")){
-...
+    		}
     		return (additionalContentList.size() == 0);
+    	}
+    }

     * 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.tcsrdf;
     import static eu.etaxonomy.cdm.io.common.ImportHelper.NO_OVERWRITE;
-...
     //			"created_When", "updated_When", "created_Who", "updated_Who", "notes"
     //	};
     	protected static CdmSingleAttributeXmlMapperBase[] unclearMappers = new CdmSingleAttributeXmlMapperBase[]{
     	};
     	protected static CdmSingleAttributeXmlMapperBase[] unclearMappers = new CdmSingleAttributeXmlMapperBase[]{};
     	private boolean makeStandardMapper(Statement resource, Reference ref, Set<String> omitAttributes){
     		if (omitAttributes == null){
     			omitAttributes = new HashSet<String>();
     			omitAttributes = new HashSet<>();
+    		}
     		boolean result = true;
     		for (IRdfMapper mapper : standardMappers){
     			if (mapper instanceof CdmSingleAttributeMapperBase){
     				makeSingleAttributeMapper((CdmSingleAttributeRDFMapperBase)mapper, resource, ref, omitAttributes);
-...
     	private boolean makeMultipleAttributeMapper(CdmOneToManyMapper<?,?,CdmTextElementMapper> mapper, Statement parentElement, Reference ref, Set<String> omitAttributes){
     		if (omitAttributes == null){
     			omitAttributes = new HashSet<String>();
     			omitAttributes = new HashSet<>();
+    		}
     		boolean result = true;
     		String destinationAttribute = mapper.getSingleAttributeName();
     		List<Object> sourceValues = new ArrayList<Object>();
     		List<Class> classes = new ArrayList<Class>();
     		List<Object> sourceValues = new ArrayList<>();
     		List<Class> classes = new ArrayList<>();
     		for (CdmTextElementMapper singleMapper : mapper.getSingleMappers()){
     			String sourceAttribute = singleMapper.getSourceAttribute();
     			Object value = getValue(singleMapper, parentElement);
-...
     		//referenceService.saveReferenceAll(referenceMap.objects());
     		logger.info("end makeReferences ...");*/
     		return;
+    	}
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
     	 */
     	@Override
         protected boolean isIgnore(TcsRdfImportState state){
     		return (state.getConfig().getDoReferences() == IImportConfigurator.DO_REFERENCES.NONE);
+    	}
+    }

     * 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.tcsxml.in;
     import static eu.etaxonomy.cdm.io.common.ImportHelper.OBLIGATORY;
-...
     	@Override
         protected abstract void doInvoke(TcsXmlImportState state);
     //	/* (non-Javadoc)
     //	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
     //	 */
     //	@Override
     //	protected boolean doInvoke(IImportConfigurator config,
     //			Map<String, MapWrapper<? extends CdmBase>> stores){
-...
     //		return doInvoke(state);
     //	}
     	protected boolean makeStandardMapper(Element parentElement, CdmBase ref, Set<String> omitAttributes, CdmSingleAttributeXmlMapperBase[] classMappers){
     		if (omitAttributes == null){
     			omitAttributes = new HashSet<String>();
     			omitAttributes = new HashSet<>();
+    		}
     		boolean result = true;
     		for (CdmSingleAttributeXmlMapperBase mapper : classMappers){
-...
     						break;
+    					}
+    				}
     			}else if (content instanceof Text){
     				//empty Text
     				if (((Text)content).getTextNormalize().equals("")){
-...
     //		return true;
     //	}
     	protected boolean testAdditionalElements(Element parentElement, List<String> excludeList){
     		boolean result = true;
     		List<Element> list = parentElement.getChildren();
-...
     		return result;
+    	}
     	protected <T extends IdentifiableEntity> T makeReferenceType(Element element, Class<? extends T> clazz, MapWrapper<? extends T> objectMap, ResultWrapper<Boolean> success){
     		T result = null;
     		String linkType = element.getAttributeValue("linkType");
-...
     		return result;
+    	}
     	protected Reference makeAccordingTo(Element elAccordingTo, MapWrapper<Reference> referenceMap, ResultWrapper<Boolean> success){
     		Reference result = null;
     		if (elAccordingTo != null){
-...
     		return result;
+    	}
     	private Reference makeAccordingToDetailed(Element elAccordingToDetailed, MapWrapper<Reference> referenceMap, ResultWrapper<Boolean> success){
     		Reference result = null;
     		Namespace tcsNamespace = elAccordingToDetailed.getNamespace();
-...
     		return result;
+    	}
     	protected void testNoMoreElements(){
     		//TODO
     		//logger.info("testNoMoreElements Not yet implemented");
+    	}
     	@SuppressWarnings("unchecked")
     	protected TeamOrPersonBase<?> makeNameCitation(Element elNameCitation, MapWrapper<Person> authorMap, ResultWrapper<Boolean> success){
     		TeamOrPersonBase<?> result = null;
-...
+    		}
+    	}
     	protected Integer getIntegerYear(String year){
     		try {
     			Integer result = Integer.valueOf(year);
-...
     		} else {
     			return ref;
+    		}
+    	}
     	protected void makeTypification(TaxonName name, Element elTypifiacation, ResultWrapper<Boolean> success){
     		if (elTypifiacation != null){

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Revision 379eb203

Added by Andreas Müller over 3 years ago