cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/tcs/TcsReferenceIO.java

   1 /**
   2  *
   3  */
   4 package eu.etaxonomy.cdm.io.tcs;
   5
   6 import static eu.etaxonomy.cdm.io.common.ImportHelper.OBLIGATORY;
   7 import static eu.etaxonomy.cdm.io.common.ImportHelper.OVERWRITE;
   8
   9 import java.util.HashSet;
  10 import java.util.List;
  11 import java.util.Map;
  12 import java.util.Set;
  13
  14 import org.apache.log4j.Logger;
  15 import org.jdom.Attribute;
  16 import org.jdom.Element;
  17 import org.jdom.Namespace;
  18
  19 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  20 import eu.etaxonomy.cdm.api.service.IReferenceService;
  21 import eu.etaxonomy.cdm.common.CdmUtils;
  22 import eu.etaxonomy.cdm.common.XmlHelp;
  23 import eu.etaxonomy.cdm.io.common.ICdmIO;
  24 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  25 import eu.etaxonomy.cdm.io.common.ImportHelper;
  26 import eu.etaxonomy.cdm.io.common.MapWrapper;
  27 import eu.etaxonomy.cdm.model.agent.Team;
  28 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  29 import eu.etaxonomy.cdm.model.common.CdmBase;
  30 import eu.etaxonomy.cdm.model.common.TimePeriod;
  31 import eu.etaxonomy.cdm.model.reference.Article;
  32 import eu.etaxonomy.cdm.model.reference.Book;
  33 import eu.etaxonomy.cdm.model.reference.BookSection;
  34 import eu.etaxonomy.cdm.model.reference.Generic;
  35 import eu.etaxonomy.cdm.model.reference.Journal;
  36 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  37 import eu.etaxonomy.cdm.model.reference.StrictReferenceBase;
  38 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  39
  40 /**
  41  * @author a.mueller
  42  *
  43  */
  44 public class TcsReferenceIO extends TcsIoBase implements ICdmIO {
  45         private static final Logger logger = Logger.getLogger(TcsReferenceIO.class);
  46
  47         private static int modCount = 1000;
  48
  49         public TcsReferenceIO(){
  50                 super();
  51         }
  52
  53         @Override
  54         public boolean doCheck(IImportConfigurator config){
  55                 boolean result = true;
  56                 result &= checkArticlesWithoutJournal(config);
  57                 //result &= checkPartOfJournal(config);
  58
  59                 return result;
  60         }
  61
  62         private static boolean checkArticlesWithoutJournal(IImportConfigurator bmiConfig){
  63                 try {
  64                         boolean result = true;
  65                         //TODO
  66                         //                              result = firstRow = false;
  67 //                      }
  68 //
  69                         return result;
  70                 } catch (Exception e) {
  71                         e.printStackTrace();
  72                         return false;
  73                 }
  74         }
  75
  76
  77         protected static CdmIoXmlMapperBase[] standardMappers = new CdmIoXmlMapperBase[]{
  78                 //new CdmTextElementMapper("edition", "edition"),
  79                 new CdmTextElementMapper("volume", "volume"),
  80                 new CdmTextElementMapper("placePublished", "placePublished"),
  81                 new CdmTextElementMapper("publisher", "publisher"),
  82                 //new CdmTextElementMapper("isbn", "isbn"),
  83                 new CdmTextElementMapper("pages", "pages"),
  84                 //new CdmTextElementMapper("series", "series"),
  85                 //new CdmTextElementMapper("issn", "issn"),
  86                 //new CdmTextElementMapper("url", "uri")
  87         };
  88
  89         protected static CdmIoXmlMapperBase[] operationalMappers = new CdmIoXmlMapperBase[]{
  90                 new CdmUnclearMapper("year")
  91                 , new CdmUnclearMapper("title")
  92                 , new CdmUnclearMapper("shortTitle")
  93                 , new CdmUnclearMapper("publicationType")
  94                 , new CdmUnclearMapper("parentPublication")
  95                 , new CdmUnclearMapper("authorship")
  96
  97         };
  98
  99 //      protected static String[] createdAndNotesAttributes = new String[]{
 100 //                      "created_When", "updated_When", "created_Who", "updated_Who", "notes"
 101 //      };
 102
 103         protected static CdmIoXmlMapperBase[] unclearMappers = new CdmIoXmlMapperBase[]{
 104
 105         };
 106
 107
 108
 109         private boolean makeStandardMapper(Element parentElement, StrictReferenceBase ref, Set<String> omitAttributes){
 110                 if (omitAttributes == null){
 111                         omitAttributes = new HashSet<String>();
 112                 }
 113                 boolean result = true;
 114                 for (CdmIoXmlMapperBase mapper : standardMappers){
 115                         Object value = getValue(mapper, parentElement);
 116                         //write to destination
 117                         if (value != null){
 118                                 String destinationAttribute = mapper.getDestinationAttribute();
 119                                 if (! omitAttributes.contains(destinationAttribute)){
 120                                         result &= ImportHelper.addValue(value, ref, destinationAttribute, mapper.getTypeClass(), OVERWRITE, OBLIGATORY);
 121                                 }
 122                         }
 123                 }
 124                 return true;
 125         }
 126
 127         private Object getValue(CdmIoXmlMapperBase mapper, Element parentElement){
 128                 String sourceAttribute = mapper.getSourceAttribute().toLowerCase();
 129                 Namespace sourceNamespace = mapper.getSourceNamespace(parentElement);
 130                 Element child = parentElement.getChild(sourceAttribute, sourceNamespace);
 131                 if (child == null){
 132                         return null;
 133                 }
 134                 if (child.getContentSize() > 1){
 135                         logger.warn("Element is not String");
 136                 }
 137                 Object value = child.getTextTrim();
 138                 return value;
 139         }
 140
 141         @Override
 142         public boolean doInvoke(IImportConfigurator config, CdmApplicationController cdmApp,
 143                         Map<String, MapWrapper<? extends CdmBase>> stores){
 144
 145                 MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.REFERENCE_STORE);
 146                 MapWrapper<ReferenceBase> nomRefMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.NOMREF_STORE);
 147                 MapWrapper<TeamOrPersonBase> authorMap = (MapWrapper<TeamOrPersonBase>)stores.get(ICdmIO.AUTHOR_STORE);
 148
 149 //              MapWrapper<ReferenceBase> referenceStore= new MapWrapper<ReferenceBase>(null);
 150 //              MapWrapper<ReferenceBase> nomRefStore= new MapWrapper<ReferenceBase>(null);
 151
 152                 TcsImportConfigurator tcsConfig = (TcsImportConfigurator)config;
 153                 Element root = tcsConfig.getSourceRoot();
 154                 logger.info("start makeReferences ...");
 155
 156                 String tcsElementName;
 157                 Namespace tcsNamespace;
 158                 String cdmAttrName;
 159                 String value;
 160                 boolean success = true;
 161                 IReferenceService referenceService = cdmApp.getReferenceService();
 162
 163
 164                 //Map<Integer, ReferenceBase> referenceCollectionMap = new HashMap<Integer, ReferenceBase>();
 165
 166                 Namespace rdfNamespace = root.getNamespace();
 167                 String prefix = "tcom";
 168                 Namespace commonNamespace = root.getNamespace(prefix);
 169                 prefix = "tpub";
 170                 Namespace publicationNamespace = root.getNamespace(prefix);
 171
 172
 173
 174                 tcsElementName = "PublicationCitation";
 175                 tcsNamespace = publicationNamespace;
 176                 List<Element> elPublicationCitations = root.getChildren(tcsElementName, tcsNamespace);
 177
 178                 int nomRefCount = 0;
 179                 int biblioRefsCount = 0;
 180
 181                 int i = 0;
 182                 //for each taxonName
 183                 for (Element elPublicationCitation : elPublicationCitations){
 184
 185                         if ((++i % modCount) == 0){ logger.info("references handled: " + (i-1));}
 186
 187                         //create TaxonName element
 188                         String strAbout = elPublicationCitation.getAttributeValue("about", rdfNamespace);
 189
 190                         tcsElementName = "publicationType";
 191                         tcsNamespace = publicationNamespace;
 192                         String strPubType = XmlHelp.getChildAttributeValue(elPublicationCitation, tcsElementName, tcsNamespace, "resource", rdfNamespace);
 193
 194                         try {
 195                                 StrictReferenceBase ref = TcsTransformer.pubTypeStr2PubType(strPubType);
 196                                 if (ref==null){
 197                                         ref = Generic.NewInstance();
 198                                 }
 199
 200                                 Set<String> omitAttributes = null;
 201                                 makeStandardMapper(elPublicationCitation, ref, omitAttributes);
 202
 203
 204                                 tcsElementName = "authorship";
 205                                 tcsNamespace = publicationNamespace;
 206                                 String strAuthorship = elPublicationCitation.getChildText(tcsElementName, tcsNamespace);
 207                                 //TODO
 208                                 TeamOrPersonBase authorTeam = Team.NewInstance();
 209                                 authorTeam.setTitleCache(strAuthorship);
 210                                 ref.setAuthorTeam(authorTeam);
 211
 212                                 tcsElementName = "year";
 213                                 tcsNamespace = publicationNamespace;
 214                                 String strYear = elPublicationCitation.getChildText(tcsElementName, tcsNamespace);
 215                                 TimePeriod datePublished = ImportHelper.getDatePublished(strYear);
 216                                 ref.setDatePublished(datePublished);
 217
 218                                 //Reference
 219                                 //TODO
 220                                 tcsElementName = "parentPublication";
 221                                 tcsNamespace = publicationNamespace;
 222                                 String strParent = XmlHelp.getChildAttributeValue(elPublicationCitation, tcsElementName, tcsNamespace, "resource", rdfNamespace);
 223                                 ReferenceBase parent = referenceMap.get(strParent);
 224                                 if (parent != null){
 225                                         if ((ref instanceof Article) && (parent instanceof Journal)){
 226                                                 ((Article)ref).setInJournal((Journal)parent);
 227                                         }else if ((ref instanceof BookSection) && (parent instanceof Book)){
 228                                                 ((BookSection)ref).setInBook((Book)parent);
 229                                         }else{
 230                                                 logger.warn("parent type (parent: " + parent.getClass().getSimpleName() +", child("+strAbout+"): " + ref.getClass().getSimpleName() +  ")not yet implemented");
 231                                                 //ref.setParent(parent);
 232                                         }
 233                                 }
 234
 235
 236                                 //FIXME
 237                                 //nomRef and reference
 238                                 tcsElementName = "shortTitle";
 239                                 tcsNamespace = publicationNamespace;
 240                                 boolean nomRefExists = false;
 241                                 String strShortTitle = elPublicationCitation.getChildText(tcsElementName, tcsNamespace);
 242                                 if (! CdmUtils.Nz(strShortTitle).trim().equals("")){
 243                                         ref.setTitle(strShortTitle);
 244                                         nomRefMap.put(strAbout, ref);
 245                                         nomRefCount++;
 246                                         nomRefExists = true;
 247                                 }
 248
 249                                 tcsElementName = "title";
 250                                 tcsNamespace = publicationNamespace;
 251                                 String strTitle = elPublicationCitation.getChildText(tcsElementName, tcsNamespace);
 252                                 tcsNamespace = publicationNamespace;
 253                                 if (! CdmUtils.Nz(strTitle).trim().equals("")  || nomRefExists == false){
 254                                         //TODO
 255                                         StrictReferenceBase biblioRef = (StrictReferenceBase)ref.clone();
 256                                         biblioRef.setTitle(strTitle);
 257                                         referenceMap.put(strAbout, biblioRef);
 258                                         biblioRefsCount++;
 259                                 }
 260
 261                                 checkAdditionalContents(elPublicationCitation, standardMappers, operationalMappers, unclearMappers);
 262
 263
 264                                 //ImportHelper.setOriginalSource(nameBase, tcsConfig.getSourceReference(), nameId);
 265
 266                         } catch (UnknownCdmTypeException e) {
 267                                 //FIXME
 268                                 logger.warn("Name with id " + strAbout + " has unknown type " + strPubType + " and could not be saved.");
 269                                 success = false;
 270                         }
 271                 }
 272
 273                 //change conceptRef uuid
 274                 ReferenceBase sec = referenceMap.get(config.getSourceSecId());
 275                 if (sec == null){
 276                         sec = nomRefMap.get(config.getSourceSecId());
 277                 }
 278                 if (sec != null){
 279                         sec.setUuid(config.getSecUuid());
 280                         logger.info("concept reference uuid changed to: " + config.getSecUuid());
 281                 }
 282
 283
 284                 //save and store in map
 285                 logger.info("Save nomenclatural references (" + nomRefCount + ")");
 286                 referenceService.saveReferenceAll(nomRefMap.objects());
 287                 logger.info("Save bibliographical references (" + biblioRefsCount +")");
 288                 referenceService.saveReferenceAll(referenceMap.objects());
 289
 290                 //referenceService.saveReferenceAll(referenceMap.objects());
 291                 logger.info("end makeReferences ...");
 292                 return success;
 293         }
 294
 295         /* (non-Javadoc)
 296          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 297          */
 298         protected boolean isIgnore(IImportConfigurator config){
 299                 return (config.getDoReferences() == IImportConfigurator.DO_REFERENCES.NONE);
 300         }
 301
 302 }