cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcsxml/TcsXmlImportBase.java

   1 /**
   2 * 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
  10 package eu.etaxonomy.cdm.io.tcsxml;
  11
  12 import static eu.etaxonomy.cdm.io.common.ImportHelper.OBLIGATORY;
  13 import static eu.etaxonomy.cdm.io.common.ImportHelper.OVERWRITE;
  14
  15 import java.util.ArrayList;
  16 import java.util.Arrays;
  17 import java.util.HashSet;
  18 import java.util.List;
  19 import java.util.Map;
  20 import java.util.Set;
  21
  22 import org.apache.log4j.Logger;
  23 import org.jdom.Content;
  24 import org.jdom.Element;
  25 import org.jdom.Namespace;
  26 import org.jdom.Text;
  27
  28 import eu.etaxonomy.cdm.common.CdmUtils;
  29 import eu.etaxonomy.cdm.common.ResultWrapper;
  30 import eu.etaxonomy.cdm.common.XmlHelp;
  31 import eu.etaxonomy.cdm.io.common.CdmIoBase;
  32 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  33 import eu.etaxonomy.cdm.io.common.ImportHelper;
  34 import eu.etaxonomy.cdm.io.common.MapWrapper;
  35 import eu.etaxonomy.cdm.io.tcsrdf.CdmSingleAttributeXmlMapperBase;
  36 import eu.etaxonomy.cdm.model.agent.Team;
  37 import eu.etaxonomy.cdm.model.common.CdmBase;
  38 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  39 import eu.etaxonomy.cdm.model.reference.Generic;
  40 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  41
  42 /**
  43  * @author a.mueller
  44  * @created 04.08.2008
  45  * @version 1.0
  46  */
  47 public abstract class TcsXmlImportBase  extends CdmIoBase<IImportConfigurator> {
  48         private static final Logger logger = Logger.getLogger(TcsXmlImportBase.class);
  49
  50         protected static Namespace nsTcom = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/Common#");
  51         protected static Namespace nsTn = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/TaxonName#");
  52         protected static Namespace nsTgeo = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/GeographicRegion#");
  53         protected static Namespace nsTc = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/TaxonConcept#");
  54         protected static Namespace nsTpub = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/PublicationCitation#");
  55         protected static Namespace nsTpalm = Namespace.getNamespace("http://wp5.e-taxonomy.eu/import/palmae/common");
  56
  57
  58         protected abstract boolean doInvoke(TcsXmlImportState state);
  59
  60
  61         /* (non-Javadoc)
  62          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
  63          */
  64         @Override
  65         protected boolean doInvoke(IImportConfigurator config,
  66                         Map<String, MapWrapper<? extends CdmBase>> stores){
  67                 TcsXmlImportState state = ((TcsXmlImportConfigurator)config).getState();
  68                 state.setConfig((TcsXmlImportConfigurator)config);
  69                 return doInvoke(state);
  70         }
  71
  72
  73         protected boolean makeStandardMapper(Element parentElement, CdmBase ref, Set<String> omitAttributes, CdmSingleAttributeXmlMapperBase[] classMappers){
  74                 if (omitAttributes == null){
  75                         omitAttributes = new HashSet<String>();
  76                 }
  77                 boolean result = true;
  78                 for (CdmSingleAttributeXmlMapperBase mapper : classMappers){
  79                         Object value = getValue(mapper, parentElement);
  80                         //write to destination
  81                         if (value != null){
  82                                 String destinationAttribute = mapper.getDestinationAttribute();
  83                                 if (! omitAttributes.contains(destinationAttribute)){
  84                                         result &= ImportHelper.addValue(value, ref, destinationAttribute, mapper.getTypeClass(), OVERWRITE, OBLIGATORY);
  85                                 }
  86                         }
  87                 }
  88                 return true;
  89         }
  90
  91         private Object getValue(CdmSingleAttributeXmlMapperBase mapper, Element parentElement){
  92                 String sourceAttribute = mapper.getSourceAttribute();
  93                 Namespace sourceNamespace = mapper.getSourceNamespace(parentElement);
  94                 Element child = parentElement.getChild(sourceAttribute, sourceNamespace);
  95                 if (child == null){
  96                         return null;
  97                 }
  98                 if (child.getContentSize() > 1){
  99                         logger.warn("Element is not String");
 100                 }
 101                 Object value = child.getTextTrim();
 102                 return value;
 103         }
 104
 105         protected boolean checkAdditionalContents(Element parentElement, CdmSingleAttributeXmlMapperBase[] classMappers, CdmSingleAttributeXmlMapperBase[] operationalMappers, CdmSingleAttributeXmlMapperBase[] unclearMappers){
 106                 List<Content> additionalContentList = new ArrayList<Content>();
 107                 List<Content> contentList = parentElement.getContent();
 108                 List<CdmSingleAttributeXmlMapperBase> mapperList = new ArrayList<CdmSingleAttributeXmlMapperBase>();
 109
 110                 mapperList.addAll(Arrays.asList(classMappers));
 111                 mapperList.addAll(Arrays.asList(operationalMappers));
 112                 mapperList.addAll(Arrays.asList(unclearMappers));
 113
 114                 for(Content content: contentList){
 115                         boolean contentExists = false;
 116                         if (content instanceof Element){
 117                                 for (CdmSingleAttributeXmlMapperBase mapper : mapperList){
 118                                         if (mapper.mapsSource(content, parentElement)){
 119                                                 contentExists = true;
 120                                                 break;
 121                                         }
 122                                 }
 123
 124                         }else if (content instanceof Text){
 125                                 //empty Text
 126                                 if (((Text)content).getTextNormalize().equals("")){
 127                                         contentExists = true;
 128                                 }else{
 129                                         //
 130                                 }
 131                         }
 132
 133                         if (contentExists == false){
 134                                 additionalContentList.add(content);
 135                         }
 136                 }
 137                 for (Content additionalContent : additionalContentList){
 138                         logger.warn("Additional content: " +  additionalContent);
 139                 }
 140                 return (additionalContentList.size() == 0);
 141         }
 142
 143         protected Element getDataSetElement(TcsXmlImportConfigurator tcsConfig){
 144                 Element root = tcsConfig.getSourceRoot();
 145
 146                 if (! "DataSet".equals(root.getName())){
 147                         logger.error("Root element is not 'DataSet'");
 148                         return null;
 149                 }
 150                 if (tcsConfig.getTcsXmlNamespace() == null){
 151                         logger.error("No namespace defined for tcs");
 152                         return null;
 153                 }
 154                 if (! tcsConfig.getTcsXmlNamespace().equals(root.getNamespace())){
 155                         logger.error("Wrong namespace for element 'DataSet'");
 156                         return null;
 157                 }
 158                 //TODO prevent multiple elements
 159
 160                 return root;
 161         }
 162
 163 //      static public boolean checkFirstTwoFunctionElements(List<Object> objList){
 164 //              if (! (objList.get(0) instanceof TcsXmlImportConfigurator)){
 165 //                      logger.error("first method object has wrong type. Must be " + TcsXmlImportConfigurator.class.getSimpleName() + " but is " + (objList.get(0) == null ? "null": objList.get(0).getClass().getSimpleName()));
 166 //                      return false;
 167 //              }
 168 //              if (! (objList.get(1) == null) && ! (objList.get(1) instanceof Element)){
 169 //                      logger.error("first method object has wrong type. Must be " + Element.class.getSimpleName() + " but is " + (objList.get(1) == null ? "null": objList.get(1).getClass().getSimpleName()));
 170 //                      return false;
 171 //              }
 172 //              return true;
 173 //      }
 174
 175
 176         protected boolean testAdditionalElements(Element parentElement, List<String> excludeList){
 177                 boolean result = true;
 178                 List<Element> list = parentElement.getChildren();
 179                 for (Element element : list){
 180                         if (! excludeList.contains(element.getName())){
 181                                 logger.warn("Unknown element (" + element.getName() + ") in parent element (" + parentElement.getName() + ")");
 182                                 result = false;
 183                         }
 184                 }
 185                 return result;
 186         }
 187
 188
 189         protected <T extends IdentifiableEntity> T makeReferenceType(Element element, Class<? extends T> clazz, MapWrapper<? extends T> objectMap, ResultWrapper<Boolean> success){
 190                 T result = null;
 191                 String linkType = element.getAttributeValue("linkType");
 192                 String ref = element.getAttributeValue("ref");
 193                 if(ref == null && linkType == null){
 194                         result = getInstance(clazz);
 195                         if (result != null){
 196                                 String title = element.getTextNormalize();
 197                                 result.setTitleCache(title);
 198                         }
 199                 }else if (linkType == null || linkType.equals("local")){
 200                         //TODO
 201                         result = objectMap.get(ref);
 202                         if (result == null){
 203                                 logger.warn("Object (ref = " + ref + ")could not be found in WrapperMap");
 204                         }
 205                 }else if(linkType.equals("external")){
 206                         logger.warn("External link types not yet implemented");
 207                 }else if(linkType.equals("other")){
 208                         logger.warn("Other link types not yet implemented");
 209                 }else{
 210                         logger.warn("Unknown link type or missing ref");
 211                 }
 212                 if (result == null){
 213                         success.setValue(false);
 214                 }
 215                 return result;
 216         }
 217
 218
 219         protected ReferenceBase makeAccordingTo(Element elAccordingTo, MapWrapper<ReferenceBase> referenceMap, ResultWrapper<Boolean> success){
 220                 ReferenceBase result = null;
 221                 if (elAccordingTo != null){
 222                         String childName = "AccordingToDetailed";
 223                         boolean obligatory = false;
 224                         Element elAccordingToDetailed = XmlHelp.getSingleChildElement(success, elAccordingTo, childName, elAccordingTo.getNamespace(), obligatory);
 225
 226                         childName = "Simple";
 227                         obligatory = true;
 228                         Element elSimple = XmlHelp.getSingleChildElement(success, elAccordingTo, childName, elAccordingTo.getNamespace(), obligatory);
 229
 230                         if (elAccordingToDetailed != null){
 231                                 result = makeAccordingToDetailed(elAccordingToDetailed, referenceMap, success);
 232                         }else{
 233                                 result = Generic.NewInstance();
 234                                 String title = elSimple.getTextNormalize();
 235                                 result.setTitleCache(title);
 236                         }
 237                 }
 238                 return result;
 239         }
 240
 241
 242         private ReferenceBase makeAccordingToDetailed(Element elAccordingToDetailed, MapWrapper<ReferenceBase> referenceMap, ResultWrapper<Boolean> success){
 243                 ReferenceBase result = null;
 244                 Namespace tcsNamespace = elAccordingToDetailed.getNamespace();
 245                 if (elAccordingToDetailed != null){
 246                         //AuthorTeam
 247                         String childName = "AuthorTeam";
 248                         boolean obligatory = false;
 249                         Element elAuthorTeam = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
 250                         makeAccordingToAuthorTeam(elAuthorTeam, success);
 251
 252                         //PublishedIn
 253                         childName = "PublishedIn";
 254                         obligatory = false;
 255                         Element elPublishedIn = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
 256                         result = makeReferenceType(elPublishedIn, Generic.class, referenceMap, success);
 257
 258                         //MicroReference
 259                         childName = "MicroReference";
 260                         obligatory = false;
 261                         Element elMicroReference = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
 262                         String microReference = elMicroReference.getTextNormalize();
 263                         if (CdmUtils.Nz(microReference).equals("")){
 264                                 //TODO
 265                                 logger.warn("MicroReference not yet implemented for AccordingToDetailed");
 266                         }
 267                 }
 268                 return result;
 269         }
 270
 271         private Team makeAccordingToAuthorTeam(Element elAuthorTeam, ResultWrapper<Boolean> succes){
 272                 Team result = null;
 273                 if (elAuthorTeam != null){
 274                         //TODO
 275                         logger.warn("AuthorTeam not yet implemented for AccordingToDetailed");
 276                 }
 277                 return result;
 278         }
 279
 280
 281
 282 }