cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/reference/endnote/in/EndNoteImportBase.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.reference.endnote.in;
  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.CdmImportBase;
  32 import eu.etaxonomy.cdm.io.common.CdmIoBase;
  33 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  34 import eu.etaxonomy.cdm.io.common.ImportHelper;
  35 import eu.etaxonomy.cdm.io.common.MapWrapper;
  36 import eu.etaxonomy.cdm.io.tcsrdf.CdmSingleAttributeXmlMapperBase;
  37 import eu.etaxonomy.cdm.model.agent.Team;
  38 import eu.etaxonomy.cdm.model.common.CdmBase;
  39 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  40 import eu.etaxonomy.cdm.model.reference.Generic;
  41 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  42
  43 /**
  44  * @author a.mueller
  45  * @created 04.08.2008
  46  * @version 1.0
  47  */
  48 public abstract class EndNoteImportBase  extends CdmImportBase<EndnoteImportConfigurator, EndnoteImportState> {
  49         private static final Logger logger = Logger.getLogger(EndNoteImportBase.class);
  50
  51         protected static Namespace nsTcom = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/Common#");
  52         protected static Namespace nsTn = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/TaxonName#");
  53         protected static Namespace nsTgeo = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/GeographicRegion#");
  54         protected static Namespace nsTc = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/TaxonConcept#");
  55         protected static Namespace nsTpub = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/PublicationCitation#");
  56         protected static Namespace nsTpalm = Namespace.getNamespace("http://wp5.e-taxonomy.eu/import/palmae/common");
  57
  58
  59         protected abstract boolean doInvoke(EndnoteImportState state);
  60
  61
  62 //      /* (non-Javadoc)
  63 //       * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
  64 //       */
  65 //      @Override
  66 //      protected boolean doInvoke(IImportConfigurator config,
  67 //                      Map<String, MapWrapper<? extends CdmBase>> stores){
  68 //              TcsXmlImportState state = ((TcsXmlImportConfigurator)config).getState();
  69 //              state.setConfig((TcsXmlImportConfigurator)config);
  70 //              return doInvoke(state);
  71 //      }
  72
  73
  74         protected boolean makeStandardMapper(Element parentElement, CdmBase ref, Set<String> omitAttributes, CdmSingleAttributeXmlMapperBase[] classMappers){
  75                 if (omitAttributes == null){
  76                         omitAttributes = new HashSet<String>();
  77                 }
  78                 boolean result = true;
  79                 for (CdmSingleAttributeXmlMapperBase mapper : classMappers){
  80                         Object value = getValue(mapper, parentElement);
  81                         //write to destination
  82                         if (value != null){
  83                                 String destinationAttribute = mapper.getDestinationAttribute();
  84                                 if (! omitAttributes.contains(destinationAttribute)){
  85                                         result &= ImportHelper.addValue(value, ref, destinationAttribute, mapper.getTypeClass(), OVERWRITE, OBLIGATORY);
  86                                 }
  87                         }
  88                 }
  89                 return true;
  90         }
  91
  92         private Object getValue(CdmSingleAttributeXmlMapperBase mapper, Element parentElement){
  93                 String sourceAttribute = mapper.getSourceAttribute();
  94                 Namespace sourceNamespace = mapper.getSourceNamespace(parentElement);
  95                 Element child = parentElement.getChild(sourceAttribute, sourceNamespace);
  96                 if (child == null){
  97                         return null;
  98                 }
  99                 if (child.getContentSize() > 1){
 100                         logger.warn("Element is not String");
 101                 }
 102                 Object value = child.getTextTrim();
 103                 return value;
 104         }
 105
 106         protected boolean checkAdditionalContents(Element parentElement, CdmSingleAttributeXmlMapperBase[] classMappers, CdmSingleAttributeXmlMapperBase[] operationalMappers, CdmSingleAttributeXmlMapperBase[] unclearMappers){
 107                 List<Content> additionalContentList = new ArrayList<Content>();
 108                 List<Content> contentList = parentElement.getContent();
 109                 List<CdmSingleAttributeXmlMapperBase> mapperList = new ArrayList<CdmSingleAttributeXmlMapperBase>();
 110
 111                 mapperList.addAll(Arrays.asList(classMappers));
 112                 mapperList.addAll(Arrays.asList(operationalMappers));
 113                 mapperList.addAll(Arrays.asList(unclearMappers));
 114
 115                 for(Content content: contentList){
 116                         boolean contentExists = false;
 117                         if (content instanceof Element){
 118                                 for (CdmSingleAttributeXmlMapperBase mapper : mapperList){
 119                                         if (mapper.mapsSource(content, parentElement)){
 120                                                 contentExists = true;
 121                                                 break;
 122                                         }
 123                                 }
 124
 125                         }else if (content instanceof Text){
 126                                 //empty Text
 127                                 if (((Text)content).getTextNormalize().equals("")){
 128                                         contentExists = true;
 129                                 }else{
 130                                         //
 131                                 }
 132                         }
 133
 134                         if (contentExists == false){
 135                                 additionalContentList.add(content);
 136                         }
 137                 }
 138                 for (Content additionalContent : additionalContentList){
 139                         logger.warn("Additional content: " +  additionalContent);
 140                 }
 141                 return (additionalContentList.size() == 0);
 142         }
 143
 144         protected Element getXmlElement(EndnoteImportConfigurator tcsConfig){
 145                 Element root = tcsConfig.getSourceRoot();
 146
 147                 if (! "xml".equals(root.getName())){
 148                         logger.error("Root element is not 'xml'");
 149                         return null;
 150                 }
 151                 if (tcsConfig.getEndnoteNamespace() == null){
 152                         logger.error("No namespace defined for tcs");
 153                         return null;
 154                 }
 155                 if (! tcsConfig.getEndnoteNamespace().equals(root.getNamespace())){
 156                         logger.error("Wrong namespace for element 'xml'");
 157                         return null;
 158                 }
 159                 //TODO prevent multiple elements
 160
 161                 return root;
 162         }
 163
 164 //      static public boolean checkFirstTwoFunctionElements(List<Object> objList){
 165 //              if (! (objList.get(0) instanceof TcsXmlImportConfigurator)){
 166 //                      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()));
 167 //                      return false;
 168 //              }
 169 //              if (! (objList.get(1) == null) && ! (objList.get(1) instanceof Element)){
 170 //                      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()));
 171 //                      return false;
 172 //              }
 173 //              return true;
 174 //      }
 175
 176
 177         protected boolean testAdditionalElements(Element parentElement, List<String> excludeList){
 178                 boolean result = true;
 179                 List<Element> list = parentElement.getChildren();
 180                 for (Element element : list){
 181                         if (! excludeList.contains(element.getName())){
 182                                 logger.warn("Unknown element (" + element.getName() + ") in parent element (" + parentElement.getName() + ")");
 183                                 result = false;
 184                         }
 185                 }
 186                 return result;
 187         }
 188
 189
 190         protected <T extends IdentifiableEntity> T makeReferenceType(Element element, Class<? extends T> clazz, MapWrapper<? extends T> objectMap, ResultWrapper<Boolean> success){
 191                 T result = null;
 192                 String linkType = element.getAttributeValue("linkType");
 193                 String ref = element.getAttributeValue("ref");
 194                 if(ref == null && linkType == null){
 195                         result = getInstance(clazz);
 196                         if (result != null){
 197                                 String title = element.getTextNormalize();
 198                                 result.setTitleCache(title);
 199                         }
 200                 }else if (linkType == null || linkType.equals("local")){
 201                         //TODO
 202                         result = objectMap.get(ref);
 203                         if (result == null){
 204                                 logger.warn("Object (ref = " + ref + ")could not be found in WrapperMap");
 205                         }
 206                 }else if(linkType.equals("external")){
 207                         logger.warn("External link types not yet implemented");
 208                 }else if(linkType.equals("other")){
 209                         logger.warn("Other link types not yet implemented");
 210                 }else{
 211                         logger.warn("Unknown link type or missing ref");
 212                 }
 213                 if (result == null){
 214                         success.setValue(false);
 215                 }
 216                 return result;
 217         }
 218
 219
 220         protected ReferenceBase makeAccordingTo(Element elAccordingTo, MapWrapper<ReferenceBase> referenceMap, ResultWrapper<Boolean> success){
 221                 ReferenceBase result = null;
 222                 if (elAccordingTo != null){
 223                         String childName = "AccordingToDetailed";
 224                         boolean obligatory = false;
 225                         Element elAccordingToDetailed = XmlHelp.getSingleChildElement(success, elAccordingTo, childName, elAccordingTo.getNamespace(), obligatory);
 226
 227                         childName = "Simple";
 228                         obligatory = true;
 229                         Element elSimple = XmlHelp.getSingleChildElement(success, elAccordingTo, childName, elAccordingTo.getNamespace(), obligatory);
 230
 231                         if (elAccordingToDetailed != null){
 232                                 result = makeAccordingToDetailed(elAccordingToDetailed, referenceMap, success);
 233                         }else{
 234                                 result = Generic.NewInstance();
 235                                 String title = elSimple.getTextNormalize();
 236                                 result.setTitleCache(title);
 237                         }
 238                 }
 239                 return result;
 240         }
 241
 242
 243         private ReferenceBase makeAccordingToDetailed(Element elAccordingToDetailed, MapWrapper<ReferenceBase> referenceMap, ResultWrapper<Boolean> success){
 244                 ReferenceBase result = null;
 245                 Namespace tcsNamespace = elAccordingToDetailed.getNamespace();
 246                 if (elAccordingToDetailed != null){
 247                         //AuthorTeam
 248                         String childName = "AuthorTeam";
 249                         boolean obligatory = false;
 250                         Element elAuthorTeam = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
 251                         makeAccordingToAuthorTeam(elAuthorTeam, success);
 252
 253                         //PublishedIn
 254                         childName = "PublishedIn";
 255                         obligatory = false;
 256                         Element elPublishedIn = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
 257                         result = makeReferenceType(elPublishedIn, Generic.class, referenceMap, success);
 258
 259                         //MicroReference
 260                         childName = "MicroReference";
 261                         obligatory = false;
 262                         Element elMicroReference = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
 263                         String microReference = elMicroReference.getTextNormalize();
 264                         if (CdmUtils.Nz(microReference).equals("")){
 265                                 //TODO
 266                                 logger.warn("MicroReference not yet implemented for AccordingToDetailed");
 267                         }
 268                 }
 269                 return result;
 270         }
 271
 272         private Team makeAccordingToAuthorTeam(Element elAuthorTeam, ResultWrapper<Boolean> succes){
 273                 Team result = null;
 274                 if (elAuthorTeam != null){
 275                         //TODO
 276                         logger.warn("AuthorTeam not yet implemented for AccordingToDetailed");
 277                 }
 278                 return result;
 279         }
 280
 281
 282
 283 }