/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/in/SDDImport.java - Annotate - EDIT - EDIT Project Management

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cdmlib/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/in/SDDImport.java @ e123eb32

1	01be5674	Andreas Müller	/**
2	bba7e155	h.fradin	* Copyright (C) 2007 EDIT
3			* European Distributed Institute of Taxonomy
4			* http://www.e-taxonomy.eu
5			*
6			* The contents of this file are subject to the Mozilla Public License Version 1.1
7			* See LICENSE.TXT at the top of this package for the full license terms.
8			*/
9	01be5674	Andreas Müller
10	49f54e3f	Andreas Müller	package eu.etaxonomy.cdm.io.sdd.in;
11	cb85c609	h.fradin
12	14c311fb	h.fradin	import java.io.File;
13			import java.net.MalformedURLException;
14	218848c8	m.venin	import java.net.URI;
15	14c311fb	h.fradin	import java.net.URL;
16	cdbae74d	h.fradin	import java.text.SimpleDateFormat;
17	3ff51780	h.fradin	import java.util.ArrayList;
18	cdbae74d	h.fradin	import java.util.Date;
19	cb85c609	h.fradin	import java.util.HashMap;
20	cdbae74d	h.fradin	import java.util.HashSet;
21	cb85c609	h.fradin	import java.util.List;
22			import java.util.Map;
23	cdbae74d	h.fradin	import java.util.Set;
24	ee0eed2d	Andreas Müller	import java.util.UUID;
25	cb85c609	h.fradin
26	cfd73bf1	Andreas Müller	import org.apache.commons.lang.StringUtils;
27	cb85c609	h.fradin	import org.apache.log4j.Logger;
28			import org.jdom.Element;
29			import org.jdom.Namespace;
30			import org.joda.time.DateTime;
31	5acb39d8	ben.clark	import org.springframework.stereotype.Component;
32	cdbae74d	h.fradin	import org.springframework.transaction.TransactionStatus;
33	cb85c609	h.fradin
34			import eu.etaxonomy.cdm.api.service.IDescriptionService;
35	370503cf	n.hoffmann	import eu.etaxonomy.cdm.common.media.ImageInfo;
36	79c0eaa0	Andreas Müller	import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
37	75cb8a46	Andreas Kohlbecker	import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
38	1ffe3106	Andreas Müller	import eu.etaxonomy.cdm.io.common.ICdmImport;
39	cb85c609	h.fradin	import eu.etaxonomy.cdm.io.common.ImportHelper;
40	6b8ba655	Andreas Müller	import eu.etaxonomy.cdm.io.common.XmlImportBase;
41	7b6a429a	Andreas Müller	import eu.etaxonomy.cdm.io.sdd.SDDTransformer;
42	cb85c609	h.fradin	import eu.etaxonomy.cdm.model.agent.Person;
43	106caaa4	h.fradin	import eu.etaxonomy.cdm.model.agent.Team;
44	cb85c609	h.fradin	import eu.etaxonomy.cdm.model.common.Annotation;
45	cb404210	h.fradin	import eu.etaxonomy.cdm.model.common.AnnotationType;
46	cb85c609	h.fradin	import eu.etaxonomy.cdm.model.common.CdmBase;
47	fb3ea98b	h.fradin	import eu.etaxonomy.cdm.model.common.DefinedTermBase;
48	9068f64f	h.fradin	import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
49	57606ee3	Andreas Müller	import eu.etaxonomy.cdm.model.common.IdentifiableSource;
50	cb85c609	h.fradin	import eu.etaxonomy.cdm.model.common.Language;
51	bba7e155	h.fradin	import eu.etaxonomy.cdm.model.common.LanguageString;
52	5f03512e	m.venin	import eu.etaxonomy.cdm.model.common.Marker;
53			import eu.etaxonomy.cdm.model.common.MarkerType;
54	9068f64f	h.fradin	import eu.etaxonomy.cdm.model.common.Representation;
55			import eu.etaxonomy.cdm.model.common.TermBase;
56	cdbae74d	h.fradin	import eu.etaxonomy.cdm.model.common.TermVocabulary;
57			import eu.etaxonomy.cdm.model.common.VersionableEntity;
58	cb85c609	h.fradin	import eu.etaxonomy.cdm.model.description.CategoricalData;
59			import eu.etaxonomy.cdm.model.description.Feature;
60	bba7e155	h.fradin	import eu.etaxonomy.cdm.model.description.FeatureNode;
61	af1882d9	h.fradin	import eu.etaxonomy.cdm.model.description.FeatureTree;
62	cb85c609	h.fradin	import eu.etaxonomy.cdm.model.description.MeasurementUnit;
63	75cb8a46	Andreas Kohlbecker	import eu.etaxonomy.cdm.model.description.Modifier;
64	cb85c609	h.fradin	import eu.etaxonomy.cdm.model.description.QuantitativeData;
65			import eu.etaxonomy.cdm.model.description.State;
66	fb3ea98b	h.fradin	import eu.etaxonomy.cdm.model.description.StateData;
67	cb85c609	h.fradin	import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
68			import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
69			import eu.etaxonomy.cdm.model.description.TaxonDescription;
70			import eu.etaxonomy.cdm.model.description.TextData;
71	435d1ded	Andreas Müller	import eu.etaxonomy.cdm.model.description.WorkingSet;
72	75cb8a46	Andreas Kohlbecker	import eu.etaxonomy.cdm.model.location.NamedArea;
73			import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
74	14c311fb	h.fradin	import eu.etaxonomy.cdm.model.media.ImageFile;
75	9653d159	h.fradin	import eu.etaxonomy.cdm.model.media.Media;
76	14c311fb	h.fradin	import eu.etaxonomy.cdm.model.media.MediaRepresentation;
77	c7ab9b2a	h.fradin	import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
78	cdbae74d	h.fradin	import eu.etaxonomy.cdm.model.media.Rights;
79	cb85c609	h.fradin	import eu.etaxonomy.cdm.model.name.NonViralName;
80	514d0c79	h.fradin	import eu.etaxonomy.cdm.model.name.TaxonNameBase;
81	e192e06c	m.venin	import eu.etaxonomy.cdm.model.occurrence.Specimen;
82	1d36aa54	Andreas Müller	import eu.etaxonomy.cdm.model.reference.Reference;
83	f53af173	Katja Luther	import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
84	1d36aa54	Andreas Müller	import eu.etaxonomy.cdm.model.taxon.Classification;
85	5f03512e	m.venin	import eu.etaxonomy.cdm.model.taxon.Synonym;
86	75cb8a46	Andreas Kohlbecker	import eu.etaxonomy.cdm.model.taxon.Taxon;
87			import eu.etaxonomy.cdm.model.taxon.TaxonNode;
88	cb85c609	h.fradin
89	01be5674	Andreas Müller	/**
90			* @author h.fradin
91			* @created 24.10.2008
92			* @version 1.0
93			*/
94	7b6a429a	Andreas Müller	@Component("sddImport")
95	6b8ba655	Andreas Müller	public class SDDImport extends XmlImportBase<SDDImportConfigurator, SDDImportState> implements ICdmImport<SDDImportConfigurator, SDDImportState> {
96	036cf746	Andreas Müller	private static final Logger logger = Logger.getLogger(SDDImport.class);
97	cb85c609	h.fradin
98	e4a7b23e	h.fradin	private static int modCount = 1000;
99	cb85c609	h.fradin
100	ee0eed2d	Andreas Müller	private UUID uuidAnnotationTypeLocation = UUID.fromString("a3737e07-72e3-46d2-986d-fa4cf5de0b63");
101
102
103	bba7e155	h.fradin	private Map<String,Person> authors = new HashMap<String,Person>();
104			private Map<String,String> citations = new HashMap<String,String>();
105	808e5e3b	h.fradin	private Map<String,String> defaultUnitPrefixes = new HashMap<String,String>();
106	bba7e155	h.fradin	private Map<String,Person> editors = new HashMap<String,Person>();
107			private Map<String,FeatureNode> featureNodes = new HashMap<String,FeatureNode>();
108	808e5e3b	h.fradin	private Map<String,Feature> features = new HashMap<String,Feature>();
109	bba7e155	h.fradin	private Map<String,String> locations = new HashMap<String,String>();
110			private Map<String,List<CdmBase>> mediaObject_ListCdmBase = new HashMap<String,List<CdmBase>>();
111			private Map<String,String> mediaObject_Role = new HashMap<String,String>();
112	5559e194	Andreas Müller	private Map<String,Reference<?>> publications = new HashMap<String,Reference<?>>();
113	0ae635c4	m.venin	private Map<String,State> states = new HashMap<String,State>();
114	bba7e155	h.fradin	private Map<String,TaxonDescription> taxonDescriptions = new HashMap<String,TaxonDescription>();
115	5559e194	Andreas Müller	private Map<String,NonViralName<?>> taxonNameBases = new HashMap<String,NonViralName<?>>();
116	bba7e155	h.fradin	private Map<String,MeasurementUnit> units = new HashMap<String,MeasurementUnit>();
117	5f03512e	m.venin	private Map<String,TaxonNode> taxonNodes = new HashMap<String,TaxonNode>();
118	e192e06c	m.venin	private Map<String,NamedArea> namedAreas = new HashMap<String,NamedArea>();
119			private Map<String,Specimen> specimens = new HashMap<String,Specimen>();
120	fc15b32c	m.venin	private Map<String,Modifier> modifiers = new HashMap<String,Modifier>();
121
122			private Set<MarkerType> markerTypes = new HashSet<MarkerType>();
123	5559e194	Andreas Müller	private Set<TermVocabulary<?>> vocabularies = new HashSet<TermVocabulary<?>>();
124	5d556bff	h.fradin
125	fc15b32c	m.venin	private Set<Feature> descriptiveConcepts = new HashSet<Feature>();
126	cb404210	h.fradin	private Set<AnnotationType> annotationTypes = new HashSet<AnnotationType>();
127	435d1ded	Andreas Müller	// private Set<Feature> featureSet = new HashSet<Feature>();
128	5559e194	Andreas Müller	private Set<Reference<?>> sources = new HashSet<Reference<?>>();
129			private Reference<?> sec = ReferenceFactory.newDatabase();
130			private Reference<?> sourceReference = null;
131	9068f64f	h.fradin
132			private Language datasetLanguage = null;
133	435d1ded	Andreas Müller	private WorkingSet workingSet = null;
134	9068f64f	h.fradin
135			private Namespace xmlNamespace = Namespace.getNamespace("xml","http://www.w3.org/XML/1998/namespace");
136
137	808e5e3b	h.fradin	private String generatorName = "";
138			private String generatorVersion = "";
139	4f213356	m.venin
140	808e5e3b	h.fradin
141			private Set<StatisticalMeasure> statisticalMeasures = new HashSet<StatisticalMeasure>();
142			private Set<VersionableEntity> featureData = new HashSet<VersionableEntity>();
143	af1882d9	h.fradin	private Set<FeatureTree> featureTrees = new HashSet<FeatureTree>();
144	1d36aa54	Andreas Müller	private Set<Classification> classifications = new HashSet<Classification>();
145	808e5e3b	h.fradin
146			private Rights copyright = null;
147
148	2d28b538	m.venin	private int taxonNamesCount = 0;
149	e192e06c	m.venin
150	036cf746	Andreas Müller	public SDDImport(){
151	cb85c609	h.fradin	super();
152			}
153
154			@Override
155	6b2cc8fd	Andreas Müller	public boolean doCheck(SDDImportState state){
156	cb85c609	h.fradin	boolean result = true;
157			logger.warn("No check implemented for SDD");
158			return result;
159			}
160
161	5d556bff	h.fradin	// @Override
162			// public boolean doInvoke(IImportConfigurator config, Map<String, MapWrapper<? extends CdmBase>> stores){
163			@Override
164	51171c9d	Andreas Müller	public void doInvoke(SDDImportState state){
165	036cf746	Andreas Müller
166	d37cd796	ben.clark	TransactionStatus ts = startTransaction();
167	6b2cc8fd	Andreas Müller	SDDImportConfigurator sddConfig = state.getConfig();
168	1d36aa54	Andreas Müller	IProgressMonitor progressMonitor = sddConfig.getProgressMonitor();
169
170	808e5e3b	h.fradin	logger.info("start Datasets ...");
171	1d36aa54	Andreas Müller
172	cb85c609	h.fradin	// <Datasets xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://rs.tdwg.org/UBIF/2006/" xsi:schemaLocation="http://rs.tdwg.org/UBIF/2006/ ../SDD.xsd">
173			Element root = sddConfig.getSourceRoot();
174			Namespace sddNamespace = sddConfig.getSddNamespace();
175	14c311fb	h.fradin
176	e4a7b23e	h.fradin	logger.info("start TechnicalMetadata ...");
177	cb85c609	h.fradin	// <TechnicalMetadata created="2006-04-20T10:00:00">
178	808e5e3b	h.fradin	importTechnicalMetadata(root, sddNamespace, sddConfig);
179			List<Element> elDatasets = root.getChildren("Dataset",sddNamespace);
180	5559e194	Andreas Müller	// int i = 0;
181	9068f64f	h.fradin
182	808e5e3b	h.fradin	//for each Dataset
183			logger.info("start Dataset ...");
184	1d36aa54	Andreas Müller	progressMonitor.beginTask("Importing SDD data", elDatasets.size());
185	808e5e3b	h.fradin	for (Element elDataset : elDatasets){
186	51171c9d	Andreas Müller	importDataset(elDataset, sddNamespace, state);
187	1d36aa54	Andreas Müller	// if ((++i % modCount) == 0){ logger.info("dataset(s) handled: " + i);}
188			// logger.info(i + " dataset(s) handled");
189			progressMonitor.worked(1);
190	8940919e	h.fradin	}
191	d37cd796	ben.clark	commitTransaction(ts);
192	1d36aa54	Andreas Müller	progressMonitor.done();
193	218848c8	m.venin	logger.info("End of transaction");
194	51171c9d	Andreas Müller	return;
195	808e5e3b	h.fradin	}
196	cdbae74d	h.fradin
197	808e5e3b	h.fradin	/* (non-Javadoc)
198			* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
199			*/
200	6b2cc8fd	Andreas Müller	protected boolean isIgnore(SDDImportState state){
201	808e5e3b	h.fradin	return false;
202			}
203	cb85c609	h.fradin
204
205	808e5e3b	h.fradin	// associates the reference of a media object in SDD with a CdmBase Object
206			protected void associateImageWithCdmBase(String refMO, CdmBase cb){
207			if ((refMO != null) && (cb!=null)) {
208	cfd73bf1	Andreas Müller	if (! refMO.equals("")) {
209			if (! mediaObject_ListCdmBase.containsKey(refMO)) {
210	808e5e3b	h.fradin	List<CdmBase> lcb = new ArrayList<CdmBase>();
211			lcb.add(cb);
212			mediaObject_ListCdmBase.put(refMO,lcb);
213			} else {
214			List<CdmBase> lcb = mediaObject_ListCdmBase.get(refMO);
215			lcb.add(cb);
216			mediaObject_ListCdmBase.put(refMO,lcb);
217			}
218			}
219			}
220			}
221	cb85c609	h.fradin
222	808e5e3b	h.fradin	// imports information about the Dataset
223	8d3d15fd	h.fradin	protected void importDatasetRepresentation(Element parent, Namespace sddNamespace){
224	808e5e3b	h.fradin	logger.info("start Representation ...");
225			/* <Representation>
226			<Label>The Genus Viola</Label>
227			<Detail>This is an example for a very simple SDD file, representing a single description with categorical, quantitative, and text character. Compare also the "Fragment*" examples, which contain more complex examples in the form of document fragments. Intended for version="SDD 1.1".</Detail>
228			</Representation>
229			*/
230	435d1ded	Andreas Müller
231
232
233	808e5e3b	h.fradin	Element elRepresentation = parent.getChild("Representation",sddNamespace);
234			String label = (String)ImportHelper.getXmlInputValue(elRepresentation, "Label",sddNamespace);
235			String detail = (String)ImportHelper.getXmlInputValue(elRepresentation, "Detail",sddNamespace);
236	435d1ded	Andreas Müller
237			//new
238			Representation representation = Representation.NewInstance(detail, label, null, datasetLanguage);
239			workingSet.addRepresentation(representation);
240
241	20d09165	h.fradin
242	435d1ded	Andreas Müller	//old
243			// sec.setTitleCache(label, true);
244			//
245			// if (detail != null) {
246			// Annotation annotation = Annotation.NewInstance(detail, datasetLanguage);
247			// annotation.setAnnotationType(AnnotationType.EDITORIAL());
248			// sec.addAnnotation(annotation);
249			// }
250
251	cb85c609	h.fradin
252	808e5e3b	h.fradin	List<Element> listMediaObjects = elRepresentation.getChildren("MediaObject",sddNamespace);
253	9068f64f	h.fradin
254	808e5e3b	h.fradin	for (Element elMediaObject : listMediaObjects) {
255			String ref = null;
256			String role = null;
257			if (elMediaObject != null) {
258			ref = elMediaObject.getAttributeValue("ref");
259			role = elMediaObject.getAttributeValue("role");
260	cb85c609	h.fradin	}
261	808e5e3b	h.fradin	if (ref != null) {
262			if (!ref.equals("")) {
263	8d3d15fd	h.fradin	this.associateImageWithCdmBase(ref,sourceReference);
264	808e5e3b	h.fradin	this.associateImageWithCdmBase(ref,sec);
265			mediaObject_Role.put(ref,role);
266			}
267	83383bc9	h.fradin	}
268	808e5e3b	h.fradin	}
269			}
270	cb85c609	h.fradin
271	808e5e3b	h.fradin	// imports the representation (label, detail, lang) of a particular SDD element
272	51171c9d	Andreas Müller	protected void importRepresentation(Element parent, Namespace sddNamespace, VersionableEntity ve, String id, SDDImportState state){
273	808e5e3b	h.fradin	Element elRepresentation = parent.getChild("Representation",sddNamespace);
274	cfd73bf1	Andreas Müller
275	514d0c79	h.fradin	Map<Language,List<String>> langLabDet = new HashMap<Language,List<String>>();
276
277	cfd73bf1	Andreas Müller	handleRepresentationLabels(sddNamespace, elRepresentation, langLabDet);
278			handleRepresentationDetails(sddNamespace, elRepresentation, langLabDet);
279
280			if (ve instanceof TermBase) {
281			makeRepresentationForTerms((TermBase)ve, langLabDet);
282			}else if (ve instanceof Media) {
283			makeRepresentationForMedia((Media)ve, langLabDet);
284			}else if (ve instanceof IdentifiableEntity<?>) {
285			IdentifiableEntity<?> ie = (IdentifiableEntity<?>)ve;
286			makeRepresentationForIdentifiableEntity(sddNamespace, ie, elRepresentation, langLabDet);
287			if (ve instanceof IdentifiableMediaEntity<?>){
288			makeRepresentationForIdentifiableMediaEntity(parent, sddNamespace, (IdentifiableMediaEntity<?>)ve);
289	808e5e3b	h.fradin	}
290			}
291	cb85c609	h.fradin
292	218848c8	m.venin	makeRepresentationMediaObjects(sddNamespace, ve, elRepresentation);//FIXME
293	cfd73bf1	Andreas Müller
294			}
295
296
297			/**
298			* Handles the "Detail" children of representations. Adds the result to the langLabDet.
299			* @param sddNamespace
300			* @param elRepresentation
301			* @param langLabDet
302			*/
303			private void handleRepresentationDetails(Namespace sddNamespace,
304			Element elRepresentation, Map<Language, List<String>> langLabDet) {
305			List<Element> listDetails = elRepresentation.getChildren("Detail",sddNamespace);
306	514d0c79	h.fradin	for (Element elDetail : listDetails){
307	cfd73bf1	Andreas Müller	Language language = getLanguage(elDetail);
308	514d0c79	h.fradin	String role = elDetail.getAttributeValue("role");
309			String detail = elDetail.getText();
310			List<String> labDet = langLabDet.get(language);
311			labDet.add(detail);
312			labDet.add(role);
313			langLabDet.put(language, labDet);
314	808e5e3b	h.fradin	}
315	cfd73bf1	Andreas Müller	}
316	cb85c609	h.fradin
317	cfd73bf1	Andreas Müller	/**
318			* Handles the "Label" children of representations. Adds the result to the langLabDet.
319			* @param sddNamespace
320			* @param elRepresentation
321			* @param langLabDet
322			*/
323			private void handleRepresentationLabels(Namespace sddNamespace,
324			Element elRepresentation, Map<Language, List<String>> langLabDet) {
325			// <Label xml:lang="la">Viola hederacea Labill.</Label>
326			List<Element> listLabels = elRepresentation.getChildren("Label",sddNamespace);
327			for (Element elLabel : listLabels){
328			Language language = getLanguage(elLabel);
329			String label = elLabel.getText();
330			List<String> labDet = new ArrayList<String>(3);
331			labDet.add(label);
332			langLabDet.put(language, labDet);
333			}
334			}
335
336			/**
337			*
338			* @param ve
339			* @param langLabDet
340			*/
341			private void makeRepresentationForMedia(Media m, Map<Language, List<String>> langLabDet) {
342			for (Language lang : langLabDet.keySet()){
343			List<String> labDet = langLabDet.get(lang);
344			if (labDet.get(0) != null){
345	e66d9d39	Katja Luther	m.putTitle(LanguageString.NewInstance(labDet.get(0), lang));
346	cfd73bf1	Andreas Müller	}
347			if (labDet.size()>1) {
348			m.addDescription(labDet.get(1), lang);
349			}
350			}
351			}
352	5d556bff	h.fradin
353	cfd73bf1	Andreas Müller	/**
354			* Handles representations for terms. Adds one representation per language in langLabDet.
355			*
356			* @param ve
357			* @param langLabDet
358			*/
359			private void makeRepresentationForTerms(TermBase tb, Map<Language, List<String>> langLabDet) {
360			for (Language lang : langLabDet.keySet()){
361	5d556bff	h.fradin	List<String> labDet = langLabDet.get(lang);
362			if (labDet.size()>0){
363			if (labDet.size()>1) {
364			tb.addRepresentation(Representation.NewInstance(labDet.get(1), labDet.get(0), labDet.get(0), lang));
365			} else {
366			tb.addRepresentation(Representation.NewInstance(labDet.get(0), labDet.get(0), labDet.get(0), lang));
367			}
368			}
369			}
370	cfd73bf1	Andreas Müller	}
371	5d556bff	h.fradin
372
373	cfd73bf1	Andreas Müller	/**
374			* Handles the "MediaObject" children of representations.
375			* @param sddNamespace
376			* @param ve
377			* @param elRepresentation
378			*/
379	218848c8	m.venin	private void makeRepresentationMediaObjects(Namespace sddNamespace, VersionableEntity ve, Element elRepresentation) {
380	cfd73bf1	Andreas Müller	List <Element> listMediaObjects = elRepresentation.getChildren("MediaObject", sddNamespace);
381			for (Element elMediaObject : listMediaObjects) {
382			String ref = null;
383			//TODO
384			String role = null;
385			if (elMediaObject != null) {
386			ref = elMediaObject.getAttributeValue("ref");
387			role = elMediaObject.getAttributeValue("role");
388	514d0c79	h.fradin	}
389	cfd73bf1	Andreas Müller	if (StringUtils.isNotBlank(ref)) {
390			if (ve instanceof TaxonDescription) {
391			TaxonDescription td = (TaxonDescription) ve;
392	5559e194	Andreas Müller	if (td.getSources().size() > 0) {
393			this.associateImageWithCdmBase(ref, td.getSources().iterator().next().getCitation());
394	808e5e3b	h.fradin	} else {
395	5559e194	Andreas Müller	Reference<?> descriptionSource = ReferenceFactory.newGeneric();
396	218848c8	m.venin	sources.add(descriptionSource);
397	5559e194	Andreas Müller	td.addSource(null, null, descriptionSource, null);
398	cfd73bf1	Andreas Müller	this.associateImageWithCdmBase(ref,descriptionSource);
399	cb85c609	h.fradin	}
400	cfd73bf1	Andreas Müller	} else {
401			this.associateImageWithCdmBase(ref,ve);
402	cb85c609	h.fradin	}
403			}
404	808e5e3b	h.fradin	}
405	cfd73bf1	Andreas Müller	}
406	cdbae74d	h.fradin
407	cfd73bf1	Andreas Müller	/**
408			* Handles the "Links" element
409			* @param parent
410			* @param sddNamespace
411			* @param ve
412			*/
413			private void makeRepresentationForIdentifiableMediaEntity(Element parent,
414			Namespace sddNamespace, IdentifiableMediaEntity ime) {
415			Element elLinks = parent.getChild("Links",sddNamespace);
416	5f03512e	m.venin
417	cfd73bf1	Andreas Müller	if (elLinks != null) {
418	5f03512e	m.venin
419	cfd73bf1	Andreas Müller	// <Link rel="Alternate" href="http://www.diversitycampus.net/people/hagedorn"/>
420			List<Element> listLinks = elLinks.getChildren("Link", sddNamespace);
421			Media link = Media.NewInstance();
422			MediaRepresentation mr = MediaRepresentation.NewInstance();
423			int k = 0;
424			//for each Link
425			for (Element elLink : listLinks){
426	5f03512e	m.venin
427	cfd73bf1	Andreas Müller	try {
428			//TODO
429			String rel = elLink.getAttributeValue("rel");
430			String href = elLink.getAttributeValue("href");
431	1d36aa54	Andreas Müller	URI uri = new URI(href);
432			mr.addRepresentationPart(MediaRepresentationPart.NewInstance(uri, null));
433	cfd73bf1	Andreas Müller	link.addRepresentation(mr);
434			ime.addMedia(link);
435	5f03512e	m.venin
436	cfd73bf1	Andreas Müller	} catch (Exception e) {
437			//FIXME
438			logger.warn("Import of Link " + k + " failed.");
439			}
440	5f03512e	m.venin
441	cfd73bf1	Andreas Müller	if ((++k % modCount) == 0){ logger.info("Links handled: " + k);}
442	5f03512e	m.venin
443			}
444			}
445	cfd73bf1	Andreas Müller	}
446	808e5e3b	h.fradin
447	cfd73bf1	Andreas Müller	/**
448			* @param sddNamespace
449			* @param ve
450			* @param elRepresentation
451			* @param langLabDet
452			* @return
453			*/
454			private void makeRepresentationForIdentifiableEntity(Namespace sddNamespace, IdentifiableEntity<?> ie,
455			Element elRepresentation, Map<Language, List<String>> langLabDet) {
456			List<String> labDet = null;
457
458			if (ie instanceof TaxonNameBase) {
459			if (langLabDet.keySet().contains(getTermService().getLanguageByIso("la"))) {
460			labDet = langLabDet.get(getTermService().getLanguageByIso("la"));
461			} else if (langLabDet.keySet().contains(datasetLanguage)) {
462			labDet = langLabDet.get(datasetLanguage);
463			logger.info("TaxonName " + (String)ImportHelper.getXmlInputValue(elRepresentation, "Label",sddNamespace) + " is not specified as a latin name.");
464			} else {
465			labDet = langLabDet.get(langLabDet.keySet().iterator().next());
466			logger.info("TaxonName " + (String)ImportHelper.getXmlInputValue(elRepresentation, "Label",sddNamespace) + " is not specified as a latin name.");
467	808e5e3b	h.fradin	}
468	cfd73bf1	Andreas Müller	} else {
469			labDet = langLabDet.get(langLabDet.keySet().iterator().next());
470			}
471	8940919e	h.fradin
472	cfd73bf1	Andreas Müller	//FIXME labDet is != null only for TaxonNameBase
473			ie.setTitleCache(labDet.get(0), true);
474
475			if (labDet.size()>1) {
476			Annotation annotation = null;
477			if (labDet.get(1) != null) {
478			if (labDet.get(2) != null) {
479			annotation = Annotation.NewInstance(labDet.get(2) + " - " + labDet.get(1), datasetLanguage);
480			} else {
481			annotation = Annotation.NewInstance(labDet.get(1), datasetLanguage);
482	cdbae74d	h.fradin	}
483	cb85c609	h.fradin	}
484	cfd73bf1	Andreas Müller	ie.addAnnotation(annotation);
485	808e5e3b	h.fradin	}
486	cfd73bf1	Andreas Müller	return;
487			}
488	cb85c609	h.fradin
489	cfd73bf1	Andreas Müller	/**
490			* @param elLabel
491			* @return
492			*/
493			private Language getLanguage(Element elLanguage) {
494			String lang = elLanguage.getAttributeValue("lang",xmlNamespace);
495			Language language = null;
496			if (StringUtils.isNotBlank(lang)) {
497			language = getTermService().getLanguageByIso(lang.substring(0, 2));
498			} else {
499			language = datasetLanguage;
500			}
501			return language;
502	808e5e3b	h.fradin	}
503	e192e06c	m.venin
504	8940919e	h.fradin
505	808e5e3b	h.fradin	// imports the representation (label, detail, lang) of a particular SDD element
506			protected void importTechnicalMetadata(Element root, Namespace sddNamespace, SDDImportConfigurator sddConfig){
507			Element elTechnicalMetadata = root.getChild("TechnicalMetadata", sddNamespace);
508			String nameCreated = elTechnicalMetadata.getAttributeValue("created");
509			sourceReference = sddConfig.getSourceReference();
510	3ff51780	h.fradin
511	808e5e3b	h.fradin	if (nameCreated != null) {
512			if (!nameCreated.equals("")) {
513			int year = Integer.parseInt(nameCreated.substring(0,4));
514			int monthOfYear = Integer.parseInt(nameCreated.substring(5,7));
515			int dayOfMonth = Integer.parseInt(nameCreated.substring(8,10));
516			int hourOfDay = Integer.parseInt(nameCreated.substring(11,13));
517			int minuteOfHour = Integer.parseInt(nameCreated.substring(14,16));
518			int secondOfMinute = Integer.parseInt(nameCreated.substring(17,19));
519			DateTime created = new DateTime(year,monthOfYear,dayOfMonth,hourOfDay,minuteOfHour,secondOfMinute,0);
520			sourceReference.setCreated(created);
521			sec.setCreated(created);
522			}
523			}
524	8940919e	h.fradin
525	808e5e3b	h.fradin	// <Generator name="n/a, handcrafted instance document" version="n/a"/>
526			Element elGenerator = elTechnicalMetadata.getChild("Generator", sddNamespace);
527			generatorName = elGenerator.getAttributeValue("name");
528			generatorVersion = elGenerator.getAttributeValue("version");
529	bba7e155	h.fradin
530	8d3d15fd	h.fradin	sec.addAnnotation(Annotation.NewDefaultLanguageInstance(generatorName + " - " + generatorVersion));
531			sourceReference.addAnnotation(Annotation.NewDefaultLanguageInstance(generatorName + " - " + generatorVersion));
532	808e5e3b	h.fradin
533			}
534
535			// imports the complete dataset information
536	51171c9d	Andreas Müller	protected void importDataset(Element elDataset, Namespace sddNamespace, SDDImportState state){ // <Dataset xml:lang="en-us">
537
538	435d1ded	Andreas Müller	workingSet = WorkingSet.NewInstance();
539	51171c9d	Andreas Müller	importDatasetLanguage(elDataset,state);
540	8d3d15fd	h.fradin	importDatasetRepresentation(elDataset, sddNamespace);
541	808e5e3b	h.fradin	importRevisionData(elDataset, sddNamespace);
542	51171c9d	Andreas Müller	importIPRStatements(elDataset, sddNamespace, state);
543			importTaxonNames(elDataset, sddNamespace, state);
544	2669c352	Andreas Müller
545	51171c9d	Andreas Müller	importDescriptiveConcepts(elDataset, sddNamespace, state);
546			importCharacters(elDataset, sddNamespace, state);
547			importCharacterTrees(elDataset, sddNamespace, state);
548	75cb8a46	Andreas Kohlbecker
549	7b6a429a	Andreas Müller	MarkerType editorMarkerType = getMarkerType(state, SDDTransformer.uuidMarkerEditor, "editor", "Editor", "edt");
550			MarkerType geographicAreaMarkerType = getMarkerType(state, SDDTransformer.uuidMarkerSDDGeographicArea, "SDDGeographicArea", "SDDGeographicArea", "ga");
551			MarkerType descriptiveConceptMarkerType = getMarkerType(state, SDDTransformer.uuidMarkerDescriptiveConcept, "DescriptiveConcept", "Descriptive Concept", "DC");
552	75cb8a46	Andreas Kohlbecker	markerTypes.add(editorMarkerType);
553			markerTypes.add(geographicAreaMarkerType);
554			markerTypes.add(descriptiveConceptMarkerType);
555	2669c352	Andreas Müller
556	75cb8a46	Andreas Kohlbecker	//saving of all imported data into the CDM db
557	eba3394c	Andreas Kohlbecker	saveVocabularies();
558	75cb8a46	Andreas Kohlbecker	saveFeatures();
559			saveModifiers();
560			saveStates();
561			saveMarkerType();
562			saveAreas(geographicAreaMarkerType);
563			saveUnits();
564			saveStatisticalMeasure();
565			saveAnnotationType();
566	15be68cd	Andreas Müller
567	51171c9d	Andreas Müller	importCodedDescriptions(elDataset, sddNamespace, state);
568			importAgents(elDataset, sddNamespace, state);
569			importPublications(elDataset, sddNamespace, state);
570			importMediaObjects(elDataset, sddNamespace, state);
571			importTaxonHierarchies(elDataset, sddNamespace, state);
572			importGeographicAreas(elDataset, sddNamespace, state);
573			importSpecimens(elDataset,sddNamespace, state);
574	fc15b32c	m.venin
575
576			if ((authors != null)\|\|(editors != null)) {
577	808e5e3b	h.fradin	Team team = Team.NewInstance();
578	fc15b32c	m.venin	if (authors != null) {
579	cfd73bf1	Andreas Müller	for (Person author : authors.values()){
580			team.addTeamMember(author);
581			}
582	cb85c609	h.fradin	}
583	5f03512e	m.venin	if (editors != null) {
584			Marker marker = Marker.NewInstance();
585	fc15b32c	m.venin	marker.setMarkerType(editorMarkerType);
586	cfd73bf1	Andreas Müller	for (Person editor : editors.values()){
587			Person edit = editor;
588	5f03512e	m.venin	edit.addMarker(marker);
589			team.addTeamMember(edit);
590			}
591	15be68cd	Andreas Müller	}
592	8d3d15fd	h.fradin	sec.setAuthorTeam(team);
593	808e5e3b	h.fradin	sourceReference.setAuthorTeam(team);
594			}
595	cb85c609	h.fradin
596	808e5e3b	h.fradin	if (copyright != null) {
597			sourceReference.addRights(copyright);
598			sec.addRights(copyright);
599			}
600	e192e06c	m.venin
601			// Returns a CdmApplicationController created by the values of this configuration.
602			IDescriptionService descriptionService = getDescriptionService();
603	218848c8	m.venin
604	cfd73bf1	Andreas Müller	for (TaxonDescription taxonDescription : taxonDescriptions.values()){
605	e192e06c	m.venin	// Persists a Description
606			descriptionService.save(taxonDescription);
607			}
608
609	cfd73bf1	Andreas Müller	for (String ref : taxonDescriptions.keySet()){
610	808e5e3b	h.fradin	TaxonDescription td = taxonDescriptions.get(ref);
611			if (citations.containsKey(ref)) {
612	ee0eed2d	Andreas Müller	Reference<?> publication = publications.get(citations.get(ref));
613	808e5e3b	h.fradin	if (locations.containsKey(ref)) {
614	cb404210	h.fradin	Annotation location = Annotation.NewInstance(locations.get(ref), datasetLanguage);
615	ee0eed2d	Andreas Müller	//TODO move to a generic place (implemented in hurry therefore dirty)
616			AnnotationType annotationType = getAnnotationType(state, uuidAnnotationTypeLocation, "location", "location", "location", null);
617			// annotationTypes.add(annotationType); TODO necessary??
618	cb404210	h.fradin	location.setAnnotationType(annotationType);
619	cfd73bf1	Andreas Müller	(publication).addAnnotation(location);
620	808e5e3b	h.fradin	}
621	5559e194	Andreas Müller	td.addSource(null, null,publication, null);
622	808e5e3b	h.fradin	}
623			}
624			logger.info("end makeTaxonDescriptions ...");
625	75cb8a46	Andreas Kohlbecker
626	fc15b32c	m.venin	if (descriptiveConcepts != null) {
627	cfd73bf1	Andreas Müller	for (Feature feature : descriptiveConcepts) {
628	fc15b32c	m.venin	Marker marker = Marker.NewInstance();
629			marker.setMarkerType(descriptiveConceptMarkerType);
630			feature.addMarker(marker);
631			}
632			}
633	75cb8a46	Andreas Kohlbecker	saveFeatures();
634	fc15b32c	m.venin
635	5559e194	Andreas Müller	for (Reference<?> publication : publications.values()){
636	cfd73bf1	Andreas Müller	getReferenceService().save(publication);
637	5d556bff	h.fradin	}
638	218848c8	m.venin
639	5559e194	Andreas Müller	for (Reference<?> source : sources){
640	218848c8	m.venin	getReferenceService().save(source);
641			}
642	cb85c609	h.fradin
643	cfd73bf1	Andreas Müller	for (FeatureTree featureTree : featureTrees) {
644			getFeatureTreeService().save(featureTree);
645	5d556bff	h.fradin	}
646	435d1ded	Andreas Müller	getWorkingSetService().save(workingSet);
647	1d36aa54	Andreas Müller	for (Classification classification : classifications) {
648			getClassificationService().save(classification);
649	5f03512e	m.venin	}
650	cfd73bf1	Andreas Müller	for (Specimen specimen : specimens.values()) {
651	e192e06c	m.venin	getOccurrenceService().save(specimen);
652			}
653	fc15b32c	m.venin	logger.info("end of persistence ...");
654
655	51171c9d	Andreas Müller	return;
656	75cb8a46	Andreas Kohlbecker	}
657
658	eba3394c	Andreas Kohlbecker	/**
659			*
660			*/
661			private void saveVocabularies() {
662	5559e194	Andreas Müller	for (TermVocabulary<?> vocabulary : vocabularies ){
663	eba3394c	Andreas Kohlbecker	getVocabularyService().save(vocabulary);
664			}
665
666			}
667
668	75cb8a46	Andreas Kohlbecker	private void saveAnnotationType() {
669	e614a39d	Andreas Müller	for (AnnotationType annotationType: annotationTypes){
670	ee0eed2d	Andreas Müller	getTermService().saveOrUpdate(annotationType);
671	75cb8a46	Andreas Kohlbecker	}
672			}
673
674			private void saveStatisticalMeasure() {
675	e614a39d	Andreas Müller	for (StatisticalMeasure sm : statisticalMeasures){
676	75cb8a46	Andreas Kohlbecker	getTermService().save(sm);
677			}
678			}
679
680			private void saveUnits() {
681			if (units != null) {
682	e614a39d	Andreas Müller	for (MeasurementUnit unit : units.values()){
683	75cb8a46	Andreas Kohlbecker	if (unit != null) {
684			getTermService().save(unit);
685			}
686			}
687			}
688			}
689
690			private void saveAreas(MarkerType geographicAreaMarkerType) {
691	e614a39d	Andreas Müller	for (NamedArea area : namedAreas.values() ){
692	75cb8a46	Andreas Kohlbecker	Marker marker = Marker.NewInstance();
693			marker.setMarkerType(geographicAreaMarkerType);
694			area.addMarker(marker);
695			getTermService().save(area);
696			}
697			}
698
699			private void saveStates() {
700	e614a39d	Andreas Müller	for (State state : states.values() ){
701	75cb8a46	Andreas Kohlbecker	getTermService().save(state);
702			}
703			}
704
705			private void saveMarkerType() {
706	e614a39d	Andreas Müller	for (MarkerType markerType : markerTypes){
707	75cb8a46	Andreas Kohlbecker	getTermService().save(markerType);
708			}
709			}
710
711			private void saveModifiers() {
712	e614a39d	Andreas Müller	for (Modifier modifier : modifiers.values() ){
713	75cb8a46	Andreas Kohlbecker	getTermService().save(modifier);
714			}
715			}
716
717			private void saveFeatures() {
718	e614a39d	Andreas Müller	for (Feature feature : features.values() ){
719			getTermService().save(feature);
720	75cb8a46	Andreas Kohlbecker	}
721	5d556bff	h.fradin	}
722	cb85c609	h.fradin
723	5d556bff	h.fradin	// imports the default language of the dataset
724	51171c9d	Andreas Müller	protected void importDatasetLanguage(Element elDataset, SDDImportState state){
725	5d556bff	h.fradin	String nameLang = elDataset.getAttributeValue("lang",xmlNamespace);
726	514d0c79	h.fradin
727	435d1ded	Andreas Müller	if (StringUtils.isNotBlank(nameLang)) {
728	5d556bff	h.fradin	String iso = nameLang.substring(0, 2);
729			datasetLanguage = getTermService().getLanguageByIso(iso);
730			} else {
731	a2966578	Andreas Müller	datasetLanguage = Language.DEFAULT();
732	514d0c79	h.fradin	}
733	5d556bff	h.fradin	if (datasetLanguage == null) {
734	a2966578	Andreas Müller	datasetLanguage = Language.DEFAULT();
735	808e5e3b	h.fradin	}
736	5d556bff	h.fradin	}
737	e192e06c	m.venin
738	fc15b32c	m.venin	// imports the specimens
739	51171c9d	Andreas Müller	protected void importSpecimens(Element elDataset, Namespace sddNamespace, SDDImportState cdmState) {
740	e192e06c	m.venin	logger.info("start Specimens ...");
741	fc15b32c	m.venin	/* <Specimens>
742			<Specimen id="sp1">
743			<Representation>
744			<Label>TJM45337</Label>
745			</Representation>
746			</Specimen>
747			</Specimens>
748			*/
749	e192e06c	m.venin	Element elSpecimens = elDataset.getChild("Specimens",sddNamespace);
750			if (elSpecimens != null){
751			List<Element> listSpecimens = elSpecimens.getChildren("Specimen", sddNamespace);
752			for (Element elSpecimen : listSpecimens) {
753			String id = elSpecimen.getAttributeValue("id");
754	fc15b32c	m.venin	Specimen specimen = null;
755	e192e06c	m.venin	if (!id.equals("")) {
756	fc15b32c	m.venin	specimen = Specimen.NewInstance();
757			specimens.put(id,specimen);
758	51171c9d	Andreas Müller	importRepresentation(elSpecimen, sddNamespace, specimen, id, cdmState);
759	e192e06c	m.venin	}
760			}
761	fc15b32c	m.venin
762	e192e06c	m.venin	}
763			}
764	cb85c609	h.fradin
765	5d556bff	h.fradin	// imports the revision data associated with the Dataset (authors, modifications)
766			protected void importRevisionData(Element elDataset, Namespace sddNamespace){
767			// <RevisionData>
768			logger.info("start RevisionData ...");
769			Element elRevisionData = elDataset.getChild("RevisionData",sddNamespace);
770	5f03512e	m.venin	if (elRevisionData != null){
771			// <Creators>
772			Element elCreators = elRevisionData.getChild("Creators",sddNamespace);
773	fc15b32c	m.venin
774	5f03512e	m.venin	// <Agent role="aut" ref="a1"/>
775			List<Element> listAgents = elCreators.getChildren("Agent", sddNamespace);
776	fc15b32c	m.venin
777	5f03512e	m.venin	int j = 0;
778			//for each Agent
779			for (Element elAgent : listAgents){
780	fc15b32c	m.venin
781	5f03512e	m.venin	String role = elAgent.getAttributeValue("role");
782			String ref = elAgent.getAttributeValue("ref");
783			if (role.equals("aut")) {
784			if(!ref.equals("")) {
785			authors.put(ref, null);
786			}
787	5d556bff	h.fradin	}
788	5f03512e	m.venin	if (role.equals("edt")) {
789			if(!ref.equals("")) {
790			editors.put(ref, null);
791			}
792	5d556bff	h.fradin	}
793	5f03512e	m.venin	if ((++j % modCount) == 0){ logger.info("Agents handled: " + j);}
794	fc15b32c	m.venin
795	5d556bff	h.fradin	}
796	fc15b32c	m.venin
797	5f03512e	m.venin	// <DateModified>2006-04-08T00:00:00</DateModified>
798			String stringDateModified = (String)ImportHelper.getXmlInputValue(elRevisionData, "DateModified",sddNamespace);
799	fc15b32c	m.venin
800	5f03512e	m.venin	if (stringDateModified != null) {
801			SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ss");
802			Date d = null;
803			try {
804			d = sdf.parse(stringDateModified);
805			} catch(Exception e) {
806			System.err.println("Exception :");
807			e.printStackTrace();
808			}
809	fc15b32c	m.venin
810	5f03512e	m.venin	DateTime updated = null;
811			if (d != null) {
812			updated = new DateTime(d);
813			sourceReference.setUpdated(updated);
814			sec.setUpdated(updated);
815			}
816	514d0c79	h.fradin	}
817	5d556bff	h.fradin	}
818			}
819
820			// imports ipr statements associated with a dataset
821	51171c9d	Andreas Müller	protected void importIPRStatements(Element elDataset, Namespace sddNamespace, SDDImportState state){
822	5d556bff	h.fradin	// <IPRStatements>
823			logger.info("start IPRStatements ...");
824			Element elIPRStatements = elDataset.getChild("IPRStatements",sddNamespace);
825			// <IPRStatement role="Copyright">
826			if (elIPRStatements != null) {
827			List<Element> listIPRStatements = elIPRStatements.getChildren("IPRStatement", sddNamespace);
828			int j = 0;
829			//for each IPRStatement
830
831			for (Element elIPRStatement : listIPRStatements){
832
833			String role = elIPRStatement.getAttributeValue("role");
834			// <Label xml:lang="en-au">(c) 2003-2006 Centre for Occasional Botany.</Label>
835			Element elLabel = elIPRStatement.getChild("Label",sddNamespace);
836			String lang = "";
837			if (elLabel != null) {
838			lang = elLabel.getAttributeValue("lang",xmlNamespace);
839			}
840			String label = (String)ImportHelper.getXmlInputValue(elIPRStatement, "Label",sddNamespace);
841
842			if (role.equals("Copyright")) {
843			Language iprLanguage = null;
844			if (lang != null) {
845			if (!lang.equals("")) {
846			iprLanguage = getTermService().getLanguageByIso(lang.substring(0, 2));
847			} else {
848			iprLanguage = datasetLanguage;
849			}
850			}
851			if (iprLanguage == null) {
852	808e5e3b	h.fradin	iprLanguage = datasetLanguage;
853			}
854	5d556bff	h.fradin	copyright = Rights.NewInstance(label, iprLanguage);
855	808e5e3b	h.fradin	}
856	8940919e	h.fradin
857	5d556bff	h.fradin	if (copyright != null) {
858			sourceReference.addRights(copyright);
859			sec.addRights(copyright);
860			}
861	514d0c79	h.fradin
862	5d556bff	h.fradin	if ((++j % modCount) == 0){ logger.info("IPRStatements handled: " + j);}
863	514d0c79	h.fradin
864	5d556bff	h.fradin	}
865	808e5e3b	h.fradin	}
866			}
867	cb85c609	h.fradin
868	5d556bff	h.fradin	// imports the taxon names
869	51171c9d	Andreas Müller	protected void importTaxonNames(Element elDataset, Namespace sddNamespace, SDDImportState state){
870	5d556bff	h.fradin	// <TaxonNames>
871			logger.info("start TaxonNames ...");
872			Element elTaxonNames = elDataset.getChild("TaxonNames",sddNamespace);
873			// <TaxonName id="t1" uri="urn:lsid:authority:namespace:my-own-id">
874			if (elTaxonNames != null) {
875			List<Element> listTaxonNames = elTaxonNames.getChildren("TaxonName", sddNamespace);
876			int j = 0;
877			//for each TaxonName
878			for (Element elTaxonName : listTaxonNames){
879
880			String id = elTaxonName.getAttributeValue("id");
881			String uri = elTaxonName.getAttributeValue("uri");
882
883	5559e194	Andreas Müller	NonViralName<?> tnb = null;
884	5d556bff	h.fradin	if (!id.equals("")) {
885			tnb = NonViralName.NewInstance(null);
886	57606ee3	Andreas Müller	IdentifiableSource source = null;
887	5d556bff	h.fradin	if (uri != null) {
888			if (!uri.equals("")) {
889	c58d06c3	Andreas Müller	source = IdentifiableSource.NewInstance(id, "TaxonName", ReferenceFactory.newGeneric(), uri);
890	5d556bff	h.fradin	}
891			} else {
892	57606ee3	Andreas Müller	source = IdentifiableSource.NewInstance(id, "TaxonName");
893	a6a71a15	h.fradin	}
894	5d556bff	h.fradin	tnb.addSource(source);
895			taxonNameBases.put(id,tnb);
896	cb85c609	h.fradin	}
897
898	5d556bff	h.fradin	// <Representation>
899			// <Label xml:lang="la">Viola hederacea Labill.</Label>
900	51171c9d	Andreas Müller	importRepresentation(elTaxonName, sddNamespace, tnb, id, state);
901	cb85c609	h.fradin
902	5d556bff	h.fradin	if ((++j % modCount) == 0){ logger.info("TaxonNames handled: " + j);}
903	cb85c609	h.fradin
904	5d556bff	h.fradin	}
905	808e5e3b	h.fradin	}
906			}
907	cb85c609	h.fradin
908	fc15b32c	m.venin	// imports the characters (categorical, quantitative and text ; sequence characters not supported) which correspond to CDM Features
909	51171c9d	Andreas Müller	protected void importCharacters(Element elDataset, Namespace sddNamespace, SDDImportState cdmState){
910	5d556bff	h.fradin	// <Characters>
911			logger.info("start Characters ...");
912			Element elCharacters = elDataset.getChild("Characters", sddNamespace);
913	808e5e3b	h.fradin
914	5d556bff	h.fradin	// <CategoricalCharacter id="c1">
915			if (elCharacters != null) {
916	51171c9d	Andreas Müller	handleCategoricalData(sddNamespace, cdmState, elCharacters);
917			handleQuantitativeData(sddNamespace, cdmState, elCharacters);
918			handleTextCharacters(sddNamespace, cdmState, elCharacters);
919	7b6a429a	Andreas Müller	}
920	5d556bff	h.fradin
921	7b6a429a	Andreas Müller	/*for (Iterator<Feature> f = features.values().iterator() ; f.hasNext() ;){
922			featureSet.add(f.next()); //XIM Why this line ?
923			}*/
924
925	51171c9d	Andreas Müller	return;
926	5d556bff	h.fradin
927	7b6a429a	Andreas Müller	}
928	5d556bff	h.fradin
929	7b6a429a	Andreas Müller	/**
930			* @param sddNamespace
931			* @param sddConfig
932			* @param elCharacters
933			* @return
934			*/
935	51171c9d	Andreas Müller	private void handleCategoricalData(Namespace sddNamespace, SDDImportState cdmState, Element elCharacters) {
936	7b6a429a	Andreas Müller	List<Element> elCategoricalCharacters = elCharacters.getChildren("CategoricalCharacter", sddNamespace);
937			int j = 0;
938			for (Element elCategoricalCharacter : elCategoricalCharacters){
939			try {
940
941			String idCC = elCategoricalCharacter.getAttributeValue("id");
942			Feature categoricalCharacter = Feature.NewInstance();
943			categoricalCharacter.setKindOf(Feature.DESCRIPTION());
944	51171c9d	Andreas Müller	importRepresentation(elCategoricalCharacter, sddNamespace, categoricalCharacter, idCC, cdmState);
945	7b6a429a	Andreas Müller	categoricalCharacter.setSupportsCategoricalData(true);
946
947			// <States>
948			Element elStates = elCategoricalCharacter.getChild("States",sddNamespace);
949
950			// <StateDefinition id="s1">
951			List<Element> elStateDefinitions = elStates.getChildren("StateDefinition",sddNamespace);
952	2a179529	Andreas Müller	TermVocabulary<State> termVocabularyState = TermVocabulary.NewInstance(null, null, null, null);
953	eba3394c	Andreas Kohlbecker
954			vocabularies.add(termVocabularyState);
955
956	7b6a429a	Andreas Müller	int k = 0;
957			//for each StateDefinition
958			for (Element elStateDefinition : elStateDefinitions){
959	514d0c79	h.fradin
960	7b6a429a	Andreas Müller	if ((++k % modCount) == 0){ logger.info("StateDefinitions handled: " + (k-1));}
961
962			String idS = elStateDefinition.getAttributeValue("id");
963	e614a39d	Andreas Müller	State state = states.get(idS);
964			if (state == null){
965			state = State.NewInstance();
966			}else{
967			logger.debug("State duplicate found");
968			}
969	51171c9d	Andreas Müller	importRepresentation(elStateDefinition, sddNamespace, state, idS, cdmState);
970	cb85c609	h.fradin
971	7b6a429a	Andreas Müller	termVocabularyState.addTerm(state);
972			states.put(idS,state);
973			}
974			categoricalCharacter.addSupportedCategoricalEnumeration(termVocabularyState);
975			features.put(idCC, categoricalCharacter);
976	cb85c609	h.fradin
977	7b6a429a	Andreas Müller	} catch (Exception e) {
978			logger.warn("Import of CategoricalCharacter " + j + " failed.");
979	51171c9d	Andreas Müller	cdmState.setUnsuccessfull();
980	808e5e3b	h.fradin	}
981	cb85c609	h.fradin
982	7b6a429a	Andreas Müller	if ((++j % modCount) == 0){ logger.info("CategoricalCharacters handled: " + j);}
983	cb85c609	h.fradin
984	7b6a429a	Andreas Müller	}
985	51171c9d	Andreas Müller	return;
986	7b6a429a	Andreas Müller	}
987	cb85c609	h.fradin
988	7b6a429a	Andreas Müller	/**
989			* @param sddNamespace
990			* @param sddConfig
991			* @param elCharacters
992			*/
993	51171c9d	Andreas Müller	private void handleQuantitativeData(Namespace sddNamespace, SDDImportState cdmState, Element elCharacters) {
994	7b6a429a	Andreas Müller	int j;
995			// <QuantitativeCharacter id="c2">
996			List<Element> elQuantitativeCharacters = elCharacters.getChildren("QuantitativeCharacter", sddNamespace);
997			j = 0;
998			//for each QuantitativeCharacter
999			for (Element elQuantitativeCharacter : elQuantitativeCharacters){
1000	cdbae74d	h.fradin
1001	7b6a429a	Andreas Müller	try {
1002	e4a7b23e	h.fradin
1003	7b6a429a	Andreas Müller	String idQC = elQuantitativeCharacter.getAttributeValue("id");
1004	8940919e	h.fradin
1005	7b6a429a	Andreas Müller	// <Representation>
1006			// <Label>Leaf length</Label>
1007			// </Representation>
1008			Feature quantitativeCharacter = Feature.NewInstance();
1009			quantitativeCharacter.setKindOf(Feature.DESCRIPTION());
1010	51171c9d	Andreas Müller	importRepresentation(elQuantitativeCharacter, sddNamespace, quantitativeCharacter, idQC, cdmState);
1011	7b6a429a	Andreas Müller
1012			quantitativeCharacter.setSupportsQuantitativeData(true);
1013
1014			// <MeasurementUnit>
1015			// <Label role="Abbrev">m</Label>
1016			// </MeasurementUnit>
1017			Element elMeasurementUnit = elQuantitativeCharacter.getChild("MeasurementUnit",sddNamespace);
1018			String label = "";
1019			String role = "";
1020			if (elMeasurementUnit != null) {
1021			Element elLabel = elMeasurementUnit.getChild("Label",sddNamespace);
1022			role = elLabel.getAttributeValue("role");
1023			label = (String)ImportHelper.getXmlInputValue(elMeasurementUnit, "Label",sddNamespace);
1024			}
1025
1026			MeasurementUnit unit = null;
1027			if (!label.equals("")){
1028			if (role != null) {
1029			if (role.equals("Abbrev")){
1030			unit = MeasurementUnit.NewInstance(label,label,label);
1031	5d556bff	h.fradin	}
1032	7b6a429a	Andreas Müller	} else {
1033			unit = MeasurementUnit.NewInstance(label,label,label);
1034	514d0c79	h.fradin	}
1035	7b6a429a	Andreas Müller	}
1036	5d556bff	h.fradin
1037	7b6a429a	Andreas Müller	if (unit != null) {
1038			units.put(idQC, unit);
1039			}
1040	5d556bff	h.fradin
1041	7b6a429a	Andreas Müller	//<Default>
1042			// <MeasurementUnitPrefix>milli</MeasurementUnitPrefix>
1043			//</Default>
1044			Element elDefault = elQuantitativeCharacter.getChild("Default",sddNamespace);
1045			if (elDefault != null) {
1046			String measurementUnitPrefix = (String)ImportHelper.getXmlInputValue(elDefault, "MeasurementUnitPrefix",sddNamespace);
1047	cfd73bf1	Andreas Müller	if (! measurementUnitPrefix.equals("")){
1048	7b6a429a	Andreas Müller	defaultUnitPrefixes.put(idQC, measurementUnitPrefix);
1049			}
1050	808e5e3b	h.fradin	}
1051	8940919e	h.fradin
1052	7b6a429a	Andreas Müller	features.put(idQC, quantitativeCharacter);
1053	8940919e	h.fradin
1054	7b6a429a	Andreas Müller	} catch (Exception e) {
1055			//FIXME
1056			logger.warn("Import of QuantitativeCharacter " + j + " failed.");
1057	51171c9d	Andreas Müller	cdmState.setUnsuccessfull();
1058	808e5e3b	h.fradin	}
1059	e4a7b23e	h.fradin
1060	7b6a429a	Andreas Müller	if ((++j % modCount) == 0){ logger.info("QuantitativeCharacters handled: " + j);}
1061	20d09165	h.fradin
1062	7b6a429a	Andreas Müller	}
1063	51171c9d	Andreas Müller	return;
1064	7b6a429a	Andreas Müller	}
1065	20d09165	h.fradin
1066	51171c9d	Andreas Müller	private void handleTextCharacters(Namespace sddNamespace, SDDImportState cdmState, Element elCharacters) {
1067	7b6a429a	Andreas Müller	int j;
1068			// <TextCharacter id="c3">
1069			List<Element> elTextCharacters = elCharacters.getChildren("TextCharacter", sddNamespace);
1070			j = 0;
1071			//for each TextCharacter
1072			for (Element elTextCharacter : elTextCharacters){
1073	7440c566	h.fradin
1074	7b6a429a	Andreas Müller	try {
1075	3ff51780	h.fradin
1076	7b6a429a	Andreas Müller	String idTC = elTextCharacter.getAttributeValue("id");
1077	cb85c609	h.fradin
1078	7b6a429a	Andreas Müller	// <Representation>
1079			// <Label xml:lang="en">Leaf features not covered by other characters</Label>
1080			// </Representation>
1081			Feature textCharacter = Feature.NewInstance();
1082			textCharacter.setKindOf(Feature.DESCRIPTION());
1083	51171c9d	Andreas Müller	importRepresentation(elTextCharacter, sddNamespace, textCharacter, idTC, cdmState);
1084	cb85c609	h.fradin
1085	7b6a429a	Andreas Müller	textCharacter.setSupportsTextData(true);
1086	cb85c609	h.fradin
1087	7b6a429a	Andreas Müller	features.put(idTC, textCharacter);
1088	808e5e3b	h.fradin
1089	7b6a429a	Andreas Müller	} catch (Exception e) {
1090			//FIXME
1091			logger.warn("Import of TextCharacter " + j + " failed.");
1092	51171c9d	Andreas Müller	cdmState.setUnsuccessfull();
1093	cb85c609	h.fradin	}
1094	20d09165	h.fradin
1095	7b6a429a	Andreas Müller	if ((++j % modCount) == 0){ logger.info("TextCharacters handled: " + j);}
1096	514d0c79	h.fradin
1097	7b6a429a	Andreas Müller	}
1098	51171c9d	Andreas Müller	return;
1099	808e5e3b	h.fradin	}
1100
1101	fc15b32c	m.venin	// imports the descriptions of taxa
1102	51171c9d	Andreas Müller	protected void importCodedDescriptions(Element elDataset, Namespace sddNamespace, SDDImportState cdmState){
1103
1104	5d556bff	h.fradin	// <CodedDescriptions>
1105			logger.info("start CodedDescriptions ...");
1106			Element elCodedDescriptions = elDataset.getChild("CodedDescriptions",sddNamespace);
1107	4f213356	m.venin
1108	cfd73bf1	Andreas Müller	// <CodedDescription id="D101">
1109	5d556bff	h.fradin	if (elCodedDescriptions != null) {
1110			List<Element> listCodedDescriptions = elCodedDescriptions.getChildren("CodedDescription", sddNamespace);
1111			int j = 0;
1112			//for each CodedDescription
1113			for (Element elCodedDescription : listCodedDescriptions){
1114	51171c9d	Andreas Müller	handleCodedDescription(sddNamespace, cdmState, elCodedDescription, j);
1115	cfd73bf1	Andreas Müller	if ((++j % modCount) == 0){ logger.info("CodedDescriptions handled: " + j);}
1116			}
1117			}
1118	51171c9d	Andreas Müller	return;
1119	cfd73bf1	Andreas Müller	}
1120	cb85c609	h.fradin
1121	cfd73bf1	Andreas Müller	/**
1122			* @param sddNamespace
1123			* @param sddConfig
1124			* @param j
1125			* @param elCodedDescription
1126			* @return
1127			*/
1128	51171c9d	Andreas Müller	private void handleCodedDescription(Namespace sddNamespace, SDDImportState cdmState, Element elCodedDescription, int j) {
1129	cfd73bf1	Andreas Müller	try {
1130
1131			String idCD = elCodedDescription.getAttributeValue("id");
1132
1133			// <Representation>
1134			// <Label><i>Viola hederacea</i> Labill. as revised by R. Morris April 8, 2006</Label>
1135			// </Representation>
1136			TaxonDescription taxonDescription = TaxonDescription.NewInstance();
1137	4f213356	m.venin	if (!generatorName.isEmpty()){
1138			Annotation annotation = Annotation.NewInstance(generatorName, AnnotationType.TECHNICAL(),Language.DEFAULT());
1139			taxonDescription.addAnnotation(annotation);
1140			}
1141	51171c9d	Andreas Müller	importRepresentation(elCodedDescription, sddNamespace, taxonDescription, idCD, cdmState);
1142	cfd73bf1	Andreas Müller
1143			// <Scope>
1144			// <TaxonName ref="t1"/>
1145			// <Citation ref="p1" location="p. 30"/>
1146			// </Scope>
1147			Element elScope = elCodedDescription.getChild("Scope", sddNamespace);
1148			Taxon taxon;
1149			if (elScope != null) {
1150	51171c9d	Andreas Müller	taxon = handleCDScope(sddNamespace, cdmState, idCD, elScope);
1151	cfd73bf1	Andreas Müller	} else {//in case no taxon is linked to the description, a new one is created
1152	51171c9d	Andreas Müller	taxon = handleCDNoScope(sddNamespace, cdmState, elCodedDescription);
1153	cfd73bf1	Andreas Müller	}
1154	514d0c79	h.fradin
1155	cfd73bf1	Andreas Müller	// <SummaryData>
1156			Element elSummaryData = elCodedDescription.getChild("SummaryData",sddNamespace);
1157			if (elSummaryData != null) {
1158			handleSummaryCategoricalData(sddNamespace, taxonDescription, elSummaryData);
1159			handleSummaryQuantitativeData(sddNamespace, taxonDescription, elSummaryData);
1160			handleSummaryTextData(sddNamespace, taxonDescription, elSummaryData);
1161			}
1162	7440c566	h.fradin
1163	cfd73bf1	Andreas Müller	if (taxon != null) {
1164			taxon.addDescription(taxonDescription);
1165			}
1166	218848c8	m.venin	//
1167	435d1ded	Andreas Müller	workingSet.addDescription(taxonDescription);
1168
1169			//OLD taxonDescription.setDescriptiveSystem(featureSet);
1170	5d556bff	h.fradin
1171	cfd73bf1	Andreas Müller	taxonDescriptions.put(idCD, taxonDescription);//FIXME
1172	5d556bff	h.fradin
1173	cfd73bf1	Andreas Müller	} catch (Exception e) {
1174			//FIXME
1175			logger.warn("Import of CodedDescription " + j + " failed.", e);
1176	51171c9d	Andreas Müller	cdmState.setUnsuccessfull();
1177	cfd73bf1	Andreas Müller	}
1178	51171c9d	Andreas Müller	return;
1179	cfd73bf1	Andreas Müller	}
1180	808e5e3b	h.fradin
1181	cfd73bf1	Andreas Müller	/**
1182			* @param sddNamespace
1183			* @param sddConfig
1184			* @param elCodedDescription
1185			* @param taxon
1186			* @return
1187			*/
1188	51171c9d	Andreas Müller	private Taxon handleCDNoScope(Namespace sddNamespace, SDDImportState cdmState, Element elCodedDescription ) {
1189	cfd73bf1	Andreas Müller	Taxon taxon = null;
1190	5559e194	Andreas Müller	NonViralName<?> nonViralName = NonViralName.NewInstance(null);
1191	cfd73bf1	Andreas Müller	String id = new String("" + taxonNamesCount);
1192			IdentifiableSource source = IdentifiableSource.NewInstance(id, "TaxonName");
1193	51171c9d	Andreas Müller	importRepresentation(elCodedDescription, sddNamespace, nonViralName, id, cdmState);
1194	cfd73bf1	Andreas Müller
1195	51171c9d	Andreas Müller	if(cdmState.getConfig().isDoMatchTaxa()){
1196	cfd73bf1	Andreas Müller	taxon = getTaxonService().findBestMatchingTaxon(nonViralName.getTitleCache());
1197			}
1198
1199			if(taxon != null){
1200			nonViralName = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class);
1201			// taxonNameBases.put(id ,tnb);
1202			// taxonNamesCount++;
1203	218848c8	m.venin	logger.info("using existing Taxon " + taxon.getTitleCache());
1204	cfd73bf1	Andreas Müller	} else {
1205			nonViralName.addSource(source);
1206			taxonNameBases.put(id ,nonViralName);
1207			taxonNamesCount++;
1208	218848c8	m.venin	logger.info("creating new Taxon from TaxonName " + nonViralName.getTitleCache());
1209	cfd73bf1	Andreas Müller	taxon = Taxon.NewInstance(nonViralName, sec);
1210			}
1211			return taxon;
1212			}
1213	808e5e3b	h.fradin
1214	cfd73bf1	Andreas Müller	/**
1215			* @param sddNamespace
1216			* @param sddConfig
1217			* @param idCD
1218			* @param elScope
1219			* @param taxon
1220			* @return
1221			*/
1222	51171c9d	Andreas Müller	private Taxon handleCDScope(Namespace sddNamespace, SDDImportState cdmState,
1223	cfd73bf1	Andreas Müller	String idCD, Element elScope) {
1224			Taxon taxon = null;
1225			Element elTaxonName = elScope.getChild("TaxonName", sddNamespace);
1226			String ref = elTaxonName.getAttributeValue("ref");
1227	5559e194	Andreas Müller	NonViralName<?> nonViralName = taxonNameBases.get(ref);
1228	cfd73bf1	Andreas Müller
1229	51171c9d	Andreas Müller	if(cdmState.getConfig().isDoMatchTaxa()){
1230	cfd73bf1	Andreas Müller	taxon = getTaxonService().findBestMatchingTaxon(nonViralName.getTitleCache());
1231			}
1232
1233			if(taxon != null){
1234			logger.info("using existing Taxon" + taxon.getTitleCache());
1235			if(!nonViralName.getUuid().equals(taxon.getName().getUuid())){
1236			logger.warn("TaxonNameBase entity of existing taxon does not match Name in list -> replacing Name in list");
1237			nonViralName = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class);
1238			}
1239			} else {
1240	435d1ded	Andreas Müller	logger.info("creating new Taxon from TaxonName '" + nonViralName.getTitleCache()+"'");
1241	cfd73bf1	Andreas Müller	taxon = Taxon.NewInstance(nonViralName, sec);
1242			}
1243
1244			//citation
1245			Element elCitation = elScope.getChild("Citation",sddNamespace);
1246			if (elCitation != null) {
1247			String refCitation = elCitation.getAttributeValue("ref");
1248			if (! refCitation.equals("")){
1249			citations.put(idCD, refCitation);
1250			}
1251			String location = elCitation.getAttributeValue("location");
1252			if (! location.equals("")){
1253			locations.put(idCD, location);
1254			}
1255			}
1256			return taxon;
1257			}
1258	20d09165	h.fradin
1259	cfd73bf1	Andreas Müller	/**
1260			* @param sddNamespace
1261			* @param taxonDescription
1262			* @param elSummaryData
1263			*/
1264			private void handleSummaryTextData(Namespace sddNamespace,
1265			TaxonDescription taxonDescription, Element elSummaryData) {
1266			String ref;
1267			int k;
1268			// <TextChar ref="c3">
1269			List<Element> elTextChars = elSummaryData.getChildren("TextChar", sddNamespace);
1270			k = 0;
1271			//for each TextChar
1272			for (Element elTextChar : elTextChars){
1273			if ((++k % modCount) == 0){ logger.info("TextChar handled: " + (k-1));}
1274			ref = elTextChar.getAttributeValue("ref");
1275			Feature feature = features.get(ref);
1276			TextData textData = TextData.NewInstance();
1277			textData.setFeature(feature);
1278
1279			// <Content>Free form text</Content>
1280			String content = (String)ImportHelper.getXmlInputValue(elTextChar, "Content",sddNamespace);
1281	e66d9d39	Katja Luther	textData.putText(datasetLanguage, content);
1282	cfd73bf1	Andreas Müller	taxonDescription.addElement(textData);
1283			}
1284			}
1285	5d556bff	h.fradin
1286	cfd73bf1	Andreas Müller	/**
1287			* @param sddNamespace
1288			* @param taxonDescription
1289			* @param elSummaryData
1290			*/
1291			private void handleSummaryQuantitativeData(Namespace sddNamespace,
1292			TaxonDescription taxonDescription, Element elSummaryData) {
1293			String ref;
1294			int k;
1295			// <Quantitative ref="c2">
1296			List<Element> elQuantitatives = elSummaryData.getChildren("Quantitative", sddNamespace);
1297			k = 0;
1298			//for each Quantitative
1299			for (Element elQuantitative : elQuantitatives){
1300			if ((++k % modCount) == 0){ logger.warn("Quantitative handled: " + (k-1));}
1301			ref = elQuantitative.getAttributeValue("ref");
1302			Feature feature = features.get(ref);
1303			QuantitativeData quantitativeData = QuantitativeData.NewInstance();
1304			quantitativeData.setFeature(feature);
1305
1306			MeasurementUnit unit = units.get(ref);
1307			String prefix = defaultUnitPrefixes.get(ref);
1308			if (unit != null) {
1309			String u = unit.getLabel();
1310			if (prefix != null) {
1311			u = prefix + u;
1312			}
1313			unit.setLabel(u);
1314			quantitativeData.setUnit(unit);
1315			}
1316	808e5e3b	h.fradin
1317	cfd73bf1	Andreas Müller	// <Measure type="Min" value="2.3"/>
1318			List<Element> elMeasures = elQuantitative.getChildren("Measure", sddNamespace);
1319			int l = 0;
1320
1321			//for each State
1322			for (Element elMeasure : elMeasures){
1323			if ((++l % modCount) == 0){ logger.info("States handled: " + (l-1));}
1324			String type = elMeasure.getAttributeValue("type");
1325			String value = elMeasure.getAttributeValue("value");
1326			if (value.contains(",")) {
1327			value = value.replace(',', '.');
1328			}
1329			Float v = Float.parseFloat(value);
1330			//Float v = new Float(0);
1331			StatisticalMeasure t = null;
1332			if (type.equals("Min")) {
1333			t = StatisticalMeasure.MIN();
1334			} else if (type.equals("Mean")) {
1335			t = StatisticalMeasure.AVERAGE();
1336			} else if (type.equals("Max")) {
1337			t = StatisticalMeasure.MAX();
1338			} else if (type.equals("SD")) {
1339			t = StatisticalMeasure.STANDARD_DEVIATION();
1340			} else if (type.equals("N")) {
1341			t = StatisticalMeasure.SAMPLE_SIZE();
1342			} else if (type.equals("UMethLower")) {
1343			t = StatisticalMeasure.TYPICAL_LOWER_BOUNDARY();
1344			} else if (type.equals("UMethUpper")) {
1345			t = StatisticalMeasure.TYPICAL_UPPER_BOUNDARY();
1346			} else if (type.equals("Var")) {
1347			t = StatisticalMeasure.VARIANCE();
1348			} else {
1349			t = StatisticalMeasure.NewInstance(type,type,type);
1350			statisticalMeasures.add(t);
1351	cb85c609	h.fradin	}
1352
1353	cfd73bf1	Andreas Müller	StatisticalMeasurementValue statisticalValue = StatisticalMeasurementValue.NewInstance();
1354			statisticalValue.setValue(v);
1355			statisticalValue.setType(t);
1356			quantitativeData.addStatisticalValue(statisticalValue);
1357			featureData.add(statisticalValue);
1358	5d556bff	h.fradin	}
1359	cfd73bf1	Andreas Müller	taxonDescription.addElement(quantitativeData);
1360			}
1361			}
1362	514d0c79	h.fradin
1363	cfd73bf1	Andreas Müller	/**
1364			* @param sddNamespace
1365			* @param taxonDescription
1366			* @param elSummaryData
1367			*/
1368			private void handleSummaryCategoricalData(Namespace sddNamespace,
1369			TaxonDescription taxonDescription, Element elSummaryData) {
1370			String ref;
1371			// <Categorical ref="c4">
1372			List<Element> elCategoricals = elSummaryData.getChildren("Categorical", sddNamespace);
1373			int k = 0;
1374			//for each Categorical
1375			for (Element elCategorical : elCategoricals){
1376			if ((++k % modCount) == 0){ logger.warn("Categorical handled: " + (k-1));}
1377			ref = elCategorical.getAttributeValue("ref");
1378			Feature feature = features.get(ref);
1379			CategoricalData categoricalData = CategoricalData.NewInstance();
1380			categoricalData.setFeature(feature);
1381
1382			// <State ref="s3"/>
1383			List<Element> elStates = elCategorical.getChildren("State", sddNamespace);
1384			int l = 0;
1385
1386			//for each State
1387			for (Element elState : elStates){
1388			if ((++l % modCount) == 0){ logger.info("States handled: " + (l-1));}
1389			ref = elState.getAttributeValue("ref");
1390			State state = states.get(ref);
1391			if (state != null) {
1392			StateData stateData = StateData.NewInstance();
1393			stateData.setState(state);
1394			List<Element> elModifiers = elState.getChildren("Modifier", sddNamespace);
1395			for (Element elModifier : elModifiers){
1396			ref = elModifier.getAttributeValue("ref");
1397			Modifier modifier = modifiers.get(ref);
1398			if (modifier != null) {
1399			stateData.addModifier(modifier);
1400			}
1401			}
1402			categoricalData.addState(stateData);
1403			}
1404			taxonDescription.addElement(categoricalData);
1405			}
1406	808e5e3b	h.fradin	}
1407			}
1408	cdbae74d	h.fradin
1409	5d556bff	h.fradin	// imports the persons associated with the dataset creation, modification, related publications
1410	51171c9d	Andreas Müller	protected void importAgents(Element elDataset, Namespace sddNamespace, SDDImportState cdmState){
1411	5d556bff	h.fradin	// <Agents>
1412			logger.info("start Agents ...");
1413			Element elAgents = elDataset.getChild("Agents",sddNamespace);
1414	5f03512e	m.venin	if (elAgents != null) {
1415			// <Agent id="a1">
1416			List <Element> listAgents = elAgents.getChildren("Agent", sddNamespace);
1417			int j = 0;
1418			//for each Agent
1419			for (Element elAgent : listAgents){
1420	5d556bff	h.fradin
1421	5f03512e	m.venin	try {
1422	5d556bff	h.fradin
1423	5f03512e	m.venin	String idA = elAgent.getAttributeValue("id");
1424	8940919e	h.fradin
1425	5f03512e	m.venin	// <Representation>
1426			// <Label>Kevin Thiele</Label>
1427			// <Detail role="Description">Ali Baba is also known as r.a.m.</Detail>
1428			// </Representation>
1429			Person person = Person.NewInstance();
1430	51171c9d	Andreas Müller	importRepresentation(elAgent, sddNamespace, person, idA, cdmState);
1431	5f03512e	m.venin	person.addSource(IdentifiableSource.NewInstance(idA, "Agent"));
1432	cdbae74d	h.fradin
1433	5f03512e	m.venin	/*XIM <Links>
1434			Element elLinks = elAgent.getChild("Links",sddNamespace);
1435	9653d159	h.fradin
1436	5f03512e	m.venin	if (elLinks != null) {
1437	9653d159	h.fradin
1438	5f03512e	m.venin	// <Link rel="Alternate" href="http://www.diversitycampus.net/people/hagedorn"/>
1439			List<Element> listLinks = elLinks.getChildren("Link", sddNamespace);
1440			int k = 0;
1441			//for each Link
1442			for (Element elLink : listLinks){
1443	9653d159	h.fradin
1444	5f03512e	m.venin	try {
1445	e4a7b23e	h.fradin
1446	5f03512e	m.venin	String rel = elLink.getAttributeValue("rel");
1447			String href = elLink.getAttributeValue("href");
1448	9068f64f	h.fradin
1449	5f03512e	m.venin	Media link = Media.NewInstance();
1450			MediaRepresentation mr = MediaRepresentation.NewInstance();
1451			mr.addRepresentationPart(MediaRepresentationPart.NewInstance(href, null));
1452			link.addRepresentation(mr);
1453			person.addMedia(link);
1454	7440c566	h.fradin
1455	5f03512e	m.venin	} catch (Exception e) {
1456			//FIXME
1457			logger.warn("Import of Link " + k + " failed.");
1458			success = false;
1459			}
1460	cdbae74d	h.fradin
1461	5f03512e	m.venin	if ((++k % modCount) == 0){ logger.info("Links handled: " + k);}
1462	20d09165	h.fradin
1463	5f03512e	m.venin	}
1464			}
1465			*/
1466			if (authors.containsKey(idA)) {
1467			authors.put(idA,person);
1468			}
1469	cb85c609	h.fradin
1470	5f03512e	m.venin	if (editors.containsKey(idA)) {
1471			editors.put(idA, person);
1472	808e5e3b	h.fradin	}
1473	cb85c609	h.fradin
1474	5f03512e	m.venin	} catch (Exception e) {
1475			//FIXME
1476			logger.warn("Import of Agent " + j + " failed.");
1477	51171c9d	Andreas Müller	cdmState.setUnsuccessfull();
1478	514d0c79	h.fradin	}
1479	8940919e	h.fradin
1480	5f03512e	m.venin	if ((++j % modCount) == 0){ logger.info("Agents handled: " + j);}
1481	9068f64f	h.fradin
1482	5f03512e	m.venin	}
1483	5d556bff	h.fradin	}
1484	514d0c79	h.fradin	}
1485	3ff51780	h.fradin
1486	5d556bff	h.fradin	// imports publications related with the data set
1487	51171c9d	Andreas Müller	protected void importPublications(Element elDataset, Namespace sddNamespace, SDDImportState cdmState){
1488	fc15b32c	m.venin	/* <Publications>
1489			<Publication id="p112">
1490			<Representation>
1491			<Label>Gee, X. & Haa, Y. (2003). How to be happy in five minutes. Instant Gratifications, Palm Beach.</Label>
1492			</Representation>
1493			<Links>
1494			<Link rel="BasedOn" href="doi:10.1992/32311"/>
1495			<Link rel="Alternate" href="http://some.service.net/providing/bibliographic.data"/>
1496			</Links>
1497			</Publications>
1498			*/
1499	5d556bff	h.fradin	logger.info("start Publications ...");
1500			Element elPublications = elDataset.getChild("Publications",sddNamespace);
1501	9068f64f	h.fradin
1502	5d556bff	h.fradin	if (elPublications != null) {
1503			List<Element> listPublications = elPublications.getChildren("Publication", sddNamespace);
1504			int j = 0;
1505			for (Element elPublication : listPublications){
1506	9068f64f	h.fradin
1507	5d556bff	h.fradin	try {
1508	9068f64f	h.fradin
1509	5d556bff	h.fradin	String idP = elPublication.getAttributeValue("id");
1510	5559e194	Andreas Müller	Reference<?> publication = ReferenceFactory.newArticle();
1511	51171c9d	Andreas Müller	importRepresentation(elPublication, sddNamespace, publication, idP, cdmState);
1512	9068f64f	h.fradin
1513	5d556bff	h.fradin	publications.put(idP,publication);
1514	808e5e3b	h.fradin
1515	5d556bff	h.fradin	} catch (Exception e) {
1516			logger.warn("Import of Publication " + j + " failed.");
1517	51171c9d	Andreas Müller	cdmState.setUnsuccessfull();
1518	5d556bff	h.fradin	}
1519	514d0c79	h.fradin
1520	5d556bff	h.fradin	if ((++j % modCount) == 0){ logger.info("Publications handled: " + j);}
1521	514d0c79	h.fradin
1522	5d556bff	h.fradin	}
1523	9068f64f	h.fradin	}
1524	808e5e3b	h.fradin	}
1525	514d0c79	h.fradin
1526	0ae635c4	m.venin	// imports media objects such as images //FIXME check mediaobj
1527	51171c9d	Andreas Müller	protected void importMediaObjects(Element elDataset, Namespace sddNamespace, SDDImportState cdmState){
1528	5d556bff	h.fradin	// <MediaObjects>
1529			logger.info("start MediaObjects ...");
1530			Element elMediaObjects = elDataset.getChild("MediaObjects",sddNamespace);
1531
1532			if (elMediaObjects != null) {
1533			// <MediaObject id="m1">
1534			List<Element> listMediaObjects = elMediaObjects.getChildren("MediaObject", sddNamespace);
1535			int j = 0;
1536			for (Element elMO : listMediaObjects){
1537
1538			String id = "";
1539
1540			try {
1541			String idMO = elMO.getAttributeValue("id");
1542			id = idMO;
1543
1544			// <Representation>
1545			// <Label>Image description, e.g. to be used for alt-attribute in html.</Label>
1546			// </Representation>
1547			Media media = Media.NewInstance();
1548	51171c9d	Andreas Müller	importRepresentation(elMO, sddNamespace, media, idMO, cdmState);
1549	5d556bff	h.fradin
1550			// <Type>Image</Type>
1551			// <Source href="http://test.edu/test.jpg"/>
1552			String type = (String)ImportHelper.getXmlInputValue(elMO,"Type",sddNamespace);
1553
1554			if ((type != null) && (type.equals("Image"))) {
1555			Element elSource = elMO.getChild("Source",sddNamespace);
1556			String href = elSource.getAttributeValue("href");
1557
1558	370503cf	n.hoffmann	ImageInfo imageMetaData = null;
1559	5d556bff	h.fradin	ImageFile image = null;
1560			if (href.substring(0,7).equals("http://")) {
1561			try{
1562			URL url = new URL(href);
1563	df748bc6	Katja Luther
1564	370503cf	n.hoffmann	imageMetaData = ImageInfo.NewInstance(url.toURI(), 0);
1565	1d36aa54	Andreas Müller	image = ImageFile.NewInstance(url.toURI(), null, imageMetaData);
1566	5d556bff	h.fradin	} catch (MalformedURLException e) {
1567			logger.error("Malformed URL", e);
1568			}
1569			} else {
1570	51171c9d	Andreas Müller	String sns = cdmState.getConfig().getSourceNameString();
1571	5d556bff	h.fradin	File f = new File(sns);
1572			File parent = f.getParentFile();
1573	218848c8	m.venin	String fi = parent.toString() + File.separator + href;
1574	5d556bff	h.fradin	File file = new File(fi);
1575	370503cf	n.hoffmann	imageMetaData = ImageInfo.NewInstance(new URI(fi), 0); //file
1576	1d36aa54	Andreas Müller	image = ImageFile.NewInstance(file.toURI(), null, imageMetaData);
1577	808e5e3b	h.fradin	}
1578	5d556bff	h.fradin	MediaRepresentation representation = MediaRepresentation.NewInstance(imageMetaData.getMimeType(), null);
1579			representation.addRepresentationPart(image);
1580
1581			media.addRepresentation(representation);
1582
1583			ArrayList<CdmBase> lcb = (ArrayList<CdmBase>) mediaObject_ListCdmBase.get(idMO);
1584			if (lcb != null) {
1585			for (int k = 0; k < lcb.size(); k++) {
1586			if (lcb.get(k) instanceof DefinedTermBase) {
1587	5559e194	Andreas Müller	DefinedTermBase<?> dtb = (DefinedTermBase<?>) lcb.get(k);
1588	5d556bff	h.fradin	// if (lcb.get(0) instanceof DefinedTermBase) {
1589			// DefinedTermBase dtb = (DefinedTermBase) lcb.get(0);
1590			// if (dtb!=null) {
1591			// if (k == 0) {
1592			dtb.addMedia(media);
1593	5f03512e	m.venin	//System.out.println(dtb.getLabel());
1594	5d556bff	h.fradin	// } else {
1595			// Media me = (Media) media.clone();
1596			// dtb.addMedia(me);
1597			// }
1598			// }
1599	1d36aa54	Andreas Müller	} else if (lcb.get(k) instanceof Reference) {
1600	5559e194	Andreas Müller	Reference<?> rb = (Reference<?>) lcb.get(k);
1601	1d36aa54	Andreas Müller	//} else if (lcb.get(0) instanceof Reference) {
1602			//Reference rb = (Reference) lcb.get(0);
1603	5d556bff	h.fradin	// rb.setTitleCache(label);
1604			// if (rb!=null) {
1605			// if (k == 0) {
1606			rb.addMedia(media);
1607	5f03512e	m.venin	//System.out.println(rb.getTitle());
1608	5d556bff	h.fradin	// } else {
1609			// Media me = (Media) media.clone();
1610			// rb.addMedia(me);
1611			// }
1612			// }
1613	435d1ded	Andreas Müller	// else if (lcb.get(k) instanceof TaxonNameBase){
1614			// TaxonNameBase tb = (TaxonNameBase) lcb.get(k);
1615			// tb.addMedia(media);
1616			} else {
1617			logger.warn("Can't handle associated media for " + lcb.get(k).getId() + "(" + lcb.get(k).getClass().getSimpleName()+")" );
1618			}
1619	808e5e3b	h.fradin	}
1620	9068f64f	h.fradin	}
1621			}
1622	808e5e3b	h.fradin
1623	5d556bff	h.fradin	} catch (Exception e) {
1624			//FIXME
1625	e123eb32	Andreas Müller	logger.warn("Could not attach MediaObject " + j + "(SDD: " + id + ") to several objects: " + e.getMessage());
1626	51171c9d	Andreas Müller	cdmState.setUnsuccessfull();
1627	5d556bff	h.fradin	}
1628	514d0c79	h.fradin
1629	5d556bff	h.fradin	if ((++j % modCount) == 0){ logger.info("MediaObjects handled: " + j);
1630	bba7e155	h.fradin
1631	5d556bff	h.fradin	}
1632	bba7e155	h.fradin	}
1633			}
1634			}
1635
1636	fc15b32c	m.venin	// imports the <DescriptiveConcepts> block ; DescriptiveConcepts are used as nodes in CharacterTrees and Characters as leaves
1637			// but since Modifiers can be linked to DescriptiveConcepts they are stored as features with a particular Marker
1638	51171c9d	Andreas Müller	protected void importDescriptiveConcepts(Element elDataset, Namespace sddNamespace, SDDImportState state){
1639	fc15b32c	m.venin	/* <DescriptiveConcepts>
1640			<DescriptiveConcept id="dc0">
1641			<Representation>
1642			<Label>Fixed set of modifiers supported in Lucid3</Label>
1643			</Representation>
1644			<Modifiers>
1645			<Modifier id="mod1">
1646			<Representation>
1647			<Label>rarely</Label>
1648			</Representation>
1649			<ModifierClass>Frequency</ModifierClass>
1650			<ProportionRange lowerestimate="0.0" upperestimate="0.25"/>
1651			</Modifier>
1652			</Modifiers>
1653			</DescriptiveConcept>
1654			</DescriptiveConcepts>
1655			*/
1656	5d556bff	h.fradin	logger.info("start DescriptiveConcepts ...");
1657			Element elDescriptiveConcepts = elDataset.getChild("DescriptiveConcepts",sddNamespace);
1658			if (elDescriptiveConcepts != null) {
1659			List<Element> listDescriptiveConcepts = elDescriptiveConcepts.getChildren("DescriptiveConcept", sddNamespace);
1660			int j = 0;
1661	5f03512e	m.venin
1662	5d556bff	h.fradin	for (Element elDescriptiveConcept : listDescriptiveConcepts){
1663	fc15b32c	m.venin	try {
1664	892efc69	Andreas Kohlbecker	String id = elDescriptiveConcept.getAttributeValue("id");
1665	5d556bff	h.fradin	Feature feature = Feature.NewInstance();
1666			feature.setKindOf(Feature.DESCRIPTION());
1667	fc15b32c	m.venin	if (!id.equals("")) {
1668	892efc69	Andreas Kohlbecker	// <Representation>
1669			// <Label>Body</Label>
1670	51171c9d	Andreas Müller	importRepresentation(elDescriptiveConcept, sddNamespace, feature, id, state);
1671	fc15b32c	m.venin	features.put(id, feature);
1672			getTermService().save(feature);//XIM
1673			descriptiveConcepts.add(feature);
1674			// imports the modifiers
1675			Element elModifiers = elDescriptiveConcept.getChild("Modifiers", sddNamespace);
1676	892efc69	Andreas Kohlbecker	if (elModifiers !=null){
1677			List<Element> listModifiers = elModifiers.getChildren("Modifier", sddNamespace);
1678	2a179529	Andreas Müller	TermVocabulary<Modifier> termVocabularyState = TermVocabulary.NewInstance(null, null, null, null);
1679	892efc69	Andreas Kohlbecker	for (Element elModifier : listModifiers) {
1680	5f03512e	m.venin	Modifier modif = Modifier.NewInstance();
1681			String idmod = elModifier.getAttributeValue("id");
1682	51171c9d	Andreas Müller	importRepresentation(elModifier, sddNamespace, modif, idmod, state);
1683	5f03512e	m.venin	termVocabularyState.addTerm(modif);
1684	0ae635c4	m.venin	//termVocabularyStates.add(termVocabularyState);
1685	fc15b32c	m.venin	getVocabularyService().save(termVocabularyState);//XIM
1686			modifiers.put(idmod, modif);
1687	5f03512e	m.venin	}
1688	892efc69	Andreas Kohlbecker	feature.addRecommendedModifierEnumeration(termVocabularyState);
1689			}
1690	bba7e155	h.fradin
1691	fc15b32c	m.venin	}
1692			}
1693			catch (Exception e) {
1694	c0317737	Andreas Müller	logger.warn("Import of DescriptiveConcept " + j + " failed: " + e.getMessage());
1695	fc15b32c	m.venin	}
1696	5d556bff	h.fradin	if ((++j % modCount) == 0){ logger.info("DescriptiveConcepts handled: " + j);}
1697	bba7e155	h.fradin
1698	5d556bff	h.fradin	}
1699	bba7e155	h.fradin	}
1700			}
1701	fc15b32c	m.venin
1702			// imports the <CharacterTrees> block
1703	51171c9d	Andreas Müller	protected void importCharacterTrees(Element elDataset, Namespace sddNamespace, SDDImportState cdmState){
1704	5d556bff	h.fradin	// <CharacterTrees>
1705			logger.info("start CharacterTrees ...");
1706			Element elCharacterTrees = elDataset.getChild("CharacterTrees",sddNamespace);
1707	514d0c79	h.fradin
1708	5d556bff	h.fradin	if (elCharacterTrees != null) {
1709			List<Element> listCharacterTrees = elCharacterTrees.getChildren("CharacterTree", sddNamespace);
1710			int j = 0;
1711	5f03512e	m.venin	for (Element elCharacterTree : listCharacterTrees){
1712			try {
1713			Element elRepresentation = elCharacterTree.getChild("Representation",sddNamespace);
1714			String label = (String)ImportHelper.getXmlInputValue(elRepresentation,"Label",sddNamespace);
1715	0ae635c4	m.venin	//Element elDesignedFor = elCharacterTree.getChild("DesignedFor",sddNamespace);//TODO ?
1716	514d0c79	h.fradin
1717	435d1ded	Andreas Müller	FeatureTree featureTree = FeatureTree.NewInstance();
1718	51171c9d	Andreas Müller	importRepresentation(elCharacterTree, sddNamespace, featureTree, "", cdmState);
1719	435d1ded	Andreas Müller	FeatureNode root = featureTree.getRoot();
1720			List<Element> listeOfNodes = elCharacterTree.getChildren("Nodes", sddNamespace);
1721	fc15b32c	m.venin
1722			//Nodes of CharacterTrees in SDD always refer to DescriptiveConcepts
1723	435d1ded	Andreas Müller	for (Element elNodes : listeOfNodes) {
1724	2669c352	Andreas Müller	handleCharacterNodes(sddNamespace, root, elNodes);
1725	5f03512e	m.venin	}
1726	435d1ded	Andreas Müller	featureTrees.add(featureTree);
1727			if (workingSet.getDescriptiveSystem() != null){
1728			//TODO how to handle multiple
1729			logger.warn("Multiple feature trees not yet supported");
1730			}else{
1731			workingSet.setDescriptiveSystem(featureTree);
1732			}
1733	2669c352	Andreas Müller	}
1734	5f03512e	m.venin
1735			catch (Exception e) {
1736			logger.warn("Import of Character tree " + j + " failed.");
1737	51171c9d	Andreas Müller	cdmState.setUnsuccessfull();
1738	5f03512e	m.venin	}
1739			if ((++j % modCount) == 0){ logger.info("CharacterTrees handled: " + j);}
1740
1741			}
1742
1743			}
1744			}
1745
1746	2669c352	Andreas Müller	/**
1747			* @param sddNamespace
1748			* @param root
1749			* @param elNodes
1750			*/
1751			private void handleCharacterNodes(Namespace sddNamespace, FeatureNode root, Element elNodes) {
1752			List<Element> listNodes = elNodes.getChildren("Node", sddNamespace);
1753			if (listNodes != null) {
1754			for (Element elNode : listNodes){
1755			String idN = elNode.getAttributeValue("id");
1756			FeatureNode fn = null;
1757			Feature dc = null;
1758			if (idN!=null) {
1759			// DescriptiveConcepts are used as nodes in CharacterTrees
1760			Element elDescriptiveConcept = elNode.getChild("DescriptiveConcept", sddNamespace);
1761			if (elDescriptiveConcept != null){
1762			String refDC = elDescriptiveConcept.getAttributeValue("ref");
1763			dc = features.get(refDC);
1764			fn = FeatureNode.NewInstance(dc);
1765			}
1766			if (fn==null){
1767			fn = FeatureNode.NewInstance();
1768			}
1769			Element elParent = elNode.getChild("Parent", sddNamespace);
1770			// in SDD links between Nodes are referenced by the <Parent> tag
1771			if (elParent!=null){
1772			String refP = elParent.getAttributeValue("ref");
1773			if (refP!=null) {
1774			FeatureNode parent = featureNodes.get(refP);
1775			if (parent==null){
1776			root.addChild(fn); // if no parent found or the reference is broken, add the node to the root of the tree
1777			}
1778			else {
1779			parent.addChild(fn);
1780			}
1781			}
1782			}
1783			else {
1784			root.addChild(fn); // if no parent found or the reference is broken, add the node to the root of the tree
1785			}
1786			}
1787			featureNodes.put(idN, fn);
1788			}
1789			}
1790
1791			// Leaves of CharacterTrees in SDD are always CharNodes (referring to Characters)
1792			List<Element> listCharNodes = elNodes.getChildren("CharNode", sddNamespace);
1793			if (listCharNodes != null) {
1794			for (Element elCharNode : listCharNodes){
1795			Element elParent = elCharNode.getChild("Parent", sddNamespace);
1796	4f213356	m.venin	Element elCharacter = elCharNode.getChild("Character", sddNamespace);
1797			Element elDependencyRules = elCharNode.getChild("DependencyRules", sddNamespace);
1798	2669c352	Andreas Müller	FeatureNode fn = FeatureNode.NewInstance();
1799	4f213356	m.venin
1800			if (elDependencyRules!=null){
1801			Element elInapplicableIf = elCharNode.getChild("InapplicableIf", sddNamespace);
1802			if (elInapplicableIf!=null){
1803			List<Element> listStates = elInapplicableIf.getChildren("State", sddNamespace);
1804			for (Element stateElement : listStates) {
1805			String refState = stateElement.getAttributeValue("ref");
1806			if ((refState!=null)&&(!refState.equals(""))) {
1807			State state = states.get(refState);
1808			fn.addInapplicableState(state);
1809			}
1810			}
1811			}
1812			Element elOnlyapplicableIf = elCharNode.getChild("OnlyApplicableIf", sddNamespace);
1813			if (elOnlyapplicableIf!=null){
1814			List<Element> listStates = elInapplicableIf.getChildren("State", sddNamespace);
1815			for (Element stateElement : listStates) {
1816			String refState = stateElement.getAttributeValue("ref");
1817			if ((refState!=null)&&(!refState.equals(""))) {
1818			State state = states.get(refState);
1819			fn.addApplicableState(state);
1820			}
1821			}
1822			}
1823			}
1824
1825	2669c352	Andreas Müller	if (elParent!=null){
1826			String refP = elParent.getAttributeValue("ref");
1827			if ((refP!=null)&&(!refP.equals(""))) {
1828			FeatureNode parent = featureNodes.get(refP);
1829			if (parent==null){
1830			parent = root; // if no parent found or the reference is broken, add the node to the root of the tree
1831			}
1832			parent.addChild(fn);
1833			}
1834			}
1835			String refC = elCharacter.getAttributeValue("ref");
1836			if ((refC!=null)&&(!refC.equals(""))){
1837			Feature character = features.get(refC);
1838			fn.setFeature(character);
1839			featureNodes.put(refC, fn);
1840			}
1841			}
1842			}
1843			}
1844
1845	fc15b32c	m.venin	// imports the <TaxonHierarchies> block
1846	51171c9d	Andreas Müller	protected void importTaxonHierarchies(Element elDataset, Namespace sddNamespace, SDDImportState cdmState){
1847	5f03512e	m.venin
1848			logger.info("start TaxonHierarchies ...");
1849			Element elTaxonHierarchies = elDataset.getChild("TaxonHierarchies",sddNamespace);
1850
1851			if (elTaxonHierarchies != null) {
1852			List<Element> listTaxonHierarchies = elTaxonHierarchies.getChildren("TaxonHierarchy", sddNamespace);
1853			int j = 0;
1854			for (Element elTaxonHierarchy : listTaxonHierarchies){
1855			try {
1856			Element elRepresentation = elTaxonHierarchy.getChild("Representation",sddNamespace);
1857			String label = (String)ImportHelper.getXmlInputValue(elRepresentation,"Label",sddNamespace);
1858	1d36aa54	Andreas Müller	Classification classification = Classification.NewInstance(label);
1859	51171c9d	Andreas Müller	importRepresentation(elTaxonHierarchy, sddNamespace, classification, "", cdmState);
1860	fc15b32c	m.venin
1861			Element elNodes = elTaxonHierarchy.getChild("Nodes", sddNamespace); // There can be only one <Nodes> block for TaxonHierarchies
1862	5f03512e	m.venin	List<Element> listNodes = elNodes.getChildren("Node", sddNamespace);
1863	fc15b32c	m.venin
1864	5f03512e	m.venin	for (Element elNode : listNodes){
1865			String idN = elNode.getAttributeValue("id");
1866	5559e194	Andreas Müller	TaxonNameBase<?,?> tnb = null;
1867	5f03512e	m.venin	if (!idN.equals("")) {
1868			Element elTaxonName = elNode.getChild("TaxonName", sddNamespace);
1869			String refTN = elTaxonName.getAttributeValue("ref");
1870			tnb = taxonNameBases.get(refTN);
1871	fc15b32c	m.venin	Taxon taxon = (Taxon) tnb.getTaxa().iterator().next() ;
1872	5f03512e	m.venin	Element elParent = elNode.getChild("Parent", sddNamespace);
1873			if (elParent!=null){
1874			String refP = elParent.getAttributeValue("ref");
1875			if (!refP.equals("")) {
1876			TaxonNode parent = taxonNodes.get(refP);
1877	fc15b32c	m.venin	TaxonNode child = parent.addChildTaxon(taxon, sec, "", Synonym.NewInstance(tnb, sec));
1878	5f03512e	m.venin	taxonNodes.put(idN,child);
1879			}
1880			}
1881			else {
1882	1d36aa54	Andreas Müller	TaxonNode tn = classification.addChildTaxon(taxon, sec, "", Synonym.NewInstance(tnb, sec)); // if no parent found or the reference is broken, add the node to the root of the tree
1883	5f03512e	m.venin	taxonNodes.put(idN,tn);
1884			}
1885			}
1886			}
1887
1888	1d36aa54	Andreas Müller	classifications.add(classification);
1889	5f03512e	m.venin	}
1890
1891			catch (Exception e) {
1892			//FIXME
1893			logger.warn("Import of Taxon Hierarchy " + j + " failed.");
1894	51171c9d	Andreas Müller	cdmState.setUnsuccessfull();
1895	5f03512e	m.venin	}
1896
1897			if ((++j % modCount) == 0){ logger.info("TaxonHierarchies handled: " + j);}
1898
1899			}
1900
1901			}
1902			}
1903
1904
1905	fc15b32c	m.venin	// imports the <GeographicAreas> block
1906	51171c9d	Andreas Müller	protected void importGeographicAreas(Element elDataset, Namespace sddNamespace, SDDImportState cdmState) {
1907	fc15b32c	m.venin	Element elGeographicAreas = elDataset.getChild("GeographicAreas",sddNamespace);
1908			if (elGeographicAreas != null) {
1909			List<Element> listGeographicAreas = elGeographicAreas.getChildren("GeographicArea", sddNamespace);
1910	5f03512e	m.venin	int j = 0;
1911	892efc69	Andreas Kohlbecker
1912	fc15b32c	m.venin	for (Element elGeographicArea : listGeographicAreas){
1913	514d0c79	h.fradin
1914	fc15b32c	m.venin	String id = elGeographicArea.getAttributeValue("id");
1915			NamedArea na = new NamedArea();
1916	51171c9d	Andreas Müller	importRepresentation(elGeographicArea, sddNamespace, na, id, cdmState);
1917	fc15b32c	m.venin	namedAreas.put(id,na);
1918	892efc69	Andreas Kohlbecker	}
1919	fc15b32c	m.venin	if ((++j % modCount) == 0){ logger.info("GeographicAreas handled: " + j);}
1920	892efc69	Andreas Kohlbecker	}
1921			}
1922	cb85c609	h.fradin	}

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