cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx2013/TaxonXImport.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.taxonx2013;
  11
  12 import java.awt.Dimension;
  13 import java.io.File;
  14 import java.io.FileWriter;
  15 import java.io.IOException;
  16 import java.io.InputStream;
  17 import java.net.URI;
  18 import java.net.URL;
  19 import java.util.ArrayList;
  20 import java.util.HashMap;
  21 import java.util.List;
  22 import java.util.Map;
  23
  24 import javax.swing.JOptionPane;
  25 import javax.swing.JScrollPane;
  26 import javax.swing.JTextArea;
  27 import javax.xml.parsers.DocumentBuilder;
  28 import javax.xml.parsers.DocumentBuilderFactory;
  29
  30 import org.apache.commons.lang.StringUtils;
  31 import org.apache.log4j.Logger;
  32 import org.springframework.stereotype.Component;
  33 import org.springframework.transaction.TransactionStatus;
  34 import org.w3c.dom.Document;
  35
  36 import eu.etaxonomy.cdm.io.common.ICdmIO;
  37 import eu.etaxonomy.cdm.io.specimen.SpecimenImportBase;
  38 import eu.etaxonomy.cdm.model.common.CdmBase;
  39 import eu.etaxonomy.cdm.model.common.Language;
  40 import eu.etaxonomy.cdm.model.description.Feature;
  41 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  42 import eu.etaxonomy.cdm.model.name.Rank;
  43 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  44 import eu.etaxonomy.cdm.model.reference.Reference;
  45 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  46 import eu.etaxonomy.cdm.model.taxon.Classification;
  47 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  48 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  49
  50 /**
  51  * @author p.kelbert 2013
  52  */
  53 @Component
  54 public class TaxonXImport extends SpecimenImportBase<TaxonXImportConfigurator, TaxonXImportState> implements ICdmIO<TaxonXImportState> {
  55     private static final Logger logger = Logger.getLogger(TaxonXImport.class);
  56     private static String prefix = "";
  57
  58     public static String LOG_FOLDER = "C:\\Users\\pesiimport\\.cdmLibrary\\log\\taxonX\\";
  59
  60     private Classification classification = null;
  61     private Reference ref = null;
  62
  63     private TaxonXImportState taxonXstate;
  64     private TaxonXDataHolder dataHolder;
  65     private DerivedUnit derivedUnitBase;
  66
  67     private TransactionStatus tx;
  68
  69     private TaxonXXMLFieldGetter taxonXFieldGetter;
  70
  71     public TaxonXImport() {
  72         super();
  73     }
  74
  75     private Map<String,Feature> featuresMap = new HashMap<String, Feature>();
  76
  77     @Override
  78     protected boolean doCheck(TaxonXImportState state) {
  79         logger.warn("Checking not yet implemented for " + this.getClass().getSimpleName());
  80         this.taxonXstate = state;
  81         return true;
  82     }
  83
  84     /**
  85      * getClassification
  86      * asks for user interaction for decision
  87      * @param classificationName : the name of the classification we are looking for
  88      * @set the global classification object
  89      */
  90     private void setClassification() {
  91         logger.info("SET CLASSIFICATION "+classification);
  92         String classificationName = taxonXstate.getConfig().getClassificationName();
  93         String defaultClassificatioName = taxonXstate.getConfig().getImportClassificationName();
  94
  95         List<Classification> classifList = getClassificationService().list(Classification.class, null, null, null, null);
  96         Map<String,Classification> classificationMap = new HashMap<String,Classification>();
  97         ArrayList<String> nodeList = new ArrayList<String>();
  98         String citation ="";
  99         String title ="";
 100         for (Classification cla:classifList){
 101             try{
 102 //                citation = cla.getCitation().toString();
 103             }catch(Exception e){
 104                 citation="";
 105             }
 106             title=StringUtils.isBlank(cla.getTitleCache()) ? "no name" : cla.getTitleCache();
 107             if (citation.length()>title.length()){
 108                 nodeList.add(citation);
 109                 classificationMap.put(citation, cla);
 110             }
 111             else{
 112                 nodeList.add(title);
 113                 classificationMap.put(title, cla);
 114             }
 115         }
 116         boolean defaultClassificationExists = nodeList.indexOf(defaultClassificatioName)>-1;
 117         if (! defaultClassificationExists ) {
 118             nodeList.add(defaultClassificatioName);
 119         }
 120         if (nodeList.indexOf(classificationName)<0) {
 121             nodeList.add(classificationName);
 122         }
 123         final String other = "Other classification - add a new one";
 124         nodeList.add(other);
 125
 126         String s;
 127         if (defaultClassificatioName != null && defaultClassificationExists  && taxonXstate.getConfig().isAlwaysUseDefaultClassification()) {
 128             s=defaultClassificatioName;
 129         } else{
 130             JTextArea textArea = new JTextArea("Which classification do you want to use ? \nThe current reference is " + classificationName);
 131             JScrollPane scrollPane = new JScrollPane(textArea);
 132             textArea.setLineWrap(true);
 133             textArea.setWrapStyleWord(true);
 134             scrollPane.setPreferredSize( new Dimension( 600, 100 ) );
 135
 136             s = (String)JOptionPane.showInputDialog(
 137                     null,
 138                     scrollPane,
 139                     "Classification",
 140                     JOptionPane.PLAIN_MESSAGE,
 141                     null,
 142                     nodeList.toArray(),
 143                     defaultClassificatioName);
 144         }
 145         ref=getReferenceService().find(ref.getUuid());
 146         if (!classificationMap.containsKey(s)){
 147             //System.out.println("Classif inconnue ?? "+s+", "+classifDic);
 148                 Reference classificationReference = null;
 149
 150                 if (s.equalsIgnoreCase(other)){
 151                 classificationName = askForValue("classification name ?", classificationName);
 152                 classificationReference = ReferenceFactory.newDatabase();
 153                 classificationReference.setTitle(classificationName);
 154             }else if (s.equalsIgnoreCase(defaultClassificatioName)){
 155                 classificationName = defaultClassificatioName;
 156                 classificationReference = ReferenceFactory.newDatabase();
 157                 classificationReference.setTitle(classificationName);
 158             }
 159             //new classification
 160             classification = Classification.NewInstance(classificationName, classificationReference,   Language.DEFAULT());
 161             getClassificationService().saveOrUpdate(classification);
 162             refreshTransaction();
 163         }
 164         else{
 165             classification = classificationMap.get(s);
 166         }
 167         if (classification == null) {
 168             String name = taxonXstate.getConfig().getClassificationName();
 169             classification = Classification.NewInstance(name, ref,  Language.DEFAULT());
 170             if (taxonXstate.getConfig().getClassificationUuid() != null) {
 171                 classification.setUuid(taxonXstate.getConfig().getClassificationUuid());
 172             }
 173             getClassificationService().saveOrUpdate(classification);
 174             refreshTransaction();
 175         }
 176     }
 177
 178     /**
 179      * asks users for decision
 180      * @param string : the parameter name we are looking at
 181      * @param defaultValue : the default value
 182      * @return
 183      */
 184     private String askForValue(String string, String defaultValue) {
 185         JTextArea textArea = new JTextArea(string);
 186         JScrollPane scrollPane = new JScrollPane(textArea);
 187         textArea.setLineWrap(true);
 188         textArea.setWrapStyleWord(true);
 189         scrollPane.setPreferredSize( new Dimension( 600, 100 ) );
 190
 191         String s = (String)JOptionPane.showInputDialog(
 192                 null,
 193                 scrollPane,
 194                 "What should be the "+string,
 195                 JOptionPane.PLAIN_MESSAGE,
 196                 null,
 197                 null,
 198                 defaultValue);
 199
 200         return s;
 201
 202     }
 203
 204     @Override
 205     public void doInvoke(TaxonXImportState state) {
 206         taxonXstate = state;
 207         tx = startTransaction();
 208
 209         logger.info("INVOKE TaxonXImport ");
 210         URI sourceName = this.taxonXstate.getConfig().getSource();
 211
 212         //        this.taxonXstate.getConfig().getClassificationName();
 213         //        this.taxonXstate.getConfig().getClassificationUuid();
 214
 215         ref = taxonXstate.getConfig().getSourceReference();
 216
 217
 218
 219         Reference secundum = taxonXstate.getConfig().getSecundum();
 220         List<Reference> references = this.getReferenceService().list(Reference.class, null, null, null, null);
 221         boolean refFound = false;
 222         for (Reference re:references){
 223             if (re.getCitation().equalsIgnoreCase(secundum.getCitation())){
 224                 refFound = true;
 225                 secundum = re;
 226             }
 227         }
 228         if (refFound) {
 229             secundum = CdmBase.deproxy(secundum, Reference.class);
 230             taxonXstate.getConfig().setSecundum(secundum);
 231         } else {
 232             this.getReferenceService().saveOrUpdate(secundum);
 233             taxonXstate.getConfig().setSecundum(secundum);
 234         }
 235
 236
 237         Reference urlRef = taxonXstate.getConfig().getOriginalSourceURL();
 238         for (Reference re:references){
 239             if (re.getCitation().equalsIgnoreCase(urlRef.getCitation())){
 240                 urlRef=re;
 241             }
 242         }
 243         this.getReferenceService().saveOrUpdate(urlRef);
 244         urlRef=getReferenceService().find(urlRef.getUuid());
 245
 246         if(!taxonXstate.getConfig().hasAskedForHigherRank()){
 247             Rank maxRank = askForHigherRank(taxonXstate.getConfig().getNomenclaturalCode());
 248             taxonXstate.getConfig().setMaxRank(maxRank);
 249             taxonXstate.getConfig().setHasAskedForHigherRank(true);
 250         }
 251
 252
 253         String message = "go taxonx!";
 254         logger.info(message);
 255         updateProgress(this.taxonXstate, message);
 256         dataHolder = new TaxonXDataHolder();
 257
 258         DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
 259         DocumentBuilder builder;
 260         URL url;
 261
 262         try {
 263             builder = factory.newDocumentBuilder();
 264             url = sourceName.toURL();
 265             Object o = url.getContent();
 266             InputStream is = (InputStream) o;
 267             Document document = builder.parse(is);
 268
 269             taxonXFieldGetter = new TaxonXXMLFieldGetter(dataHolder, prefix, document, this, taxonXstate, classification, featuresMap);
 270             /*parse the Mods from the TaxonX file
 271              *create the appropriate Reference object
 272              */
 273             ref = taxonXFieldGetter.parseMods();
 274             //            logger.info("CLASSNAME :" +taxonXstate.getConfig().getClassificationName());
 275             setClassification();
 276             taxonXFieldGetter.updateClassification(classification);
 277             //            logger.info("classif :"+classification);
 278             taxonXFieldGetter.parseTreatment(ref,sourceName);
 279             featuresMap = taxonXFieldGetter.getFeaturesUsed();
 280
 281         }catch(Exception e){
 282             e.printStackTrace();
 283             logger.warn(e);
 284
 285             File file = new File(LOG_FOLDER + "urlTaxonX.txt");
 286             FileWriter writer;
 287             try {
 288                 writer = new FileWriter(file ,true);
 289                 writer.write(sourceName+"\n");
 290                 writer.flush();
 291                 writer.close();
 292             } catch (IOException e1) {
 293                 logger.error(e1.getMessage());
 294             }
 295
 296             logger.warn(sourceName);
 297         }
 298
 299         //TODO:check how deduplicate work (and if it works..)
 300 //        if(taxonXstate.getConfig().getLastImport()) {
 301 //            deduplicate();
 302 //        }
 303         commitTransaction(tx);
 304     }
 305
 306     public void deduplicate(){
 307         //System.out.println("DEDUPLICATE REFERENCE");
 308         getReferenceService().deduplicate(Reference.class, null,null);
 309         //System.out.println("DEDUPLICATE TAXONBASE");
 310         getTaxonService().deduplicate(TaxonBase.class, null, null);
 311         //System.out.println("DEDUP END");
 312     }
 313
 314
 315     private void refreshTransaction(){
 316         commitTransaction(tx);
 317         tx = startTransaction();
 318         ref = getReferenceService().find(ref.getUuid());
 319         classification = getClassificationService().find(classification.getUuid());
 320         try{
 321             derivedUnitBase = (DerivedUnit) getOccurrenceService().find(derivedUnitBase.getUuid());
 322         }catch(Exception e){
 323             //logger.warn("derivedunit up to date or not created yet");
 324         }
 325     }
 326
 327     /**
 328      * @return
 329      */
 330     private Rank askForHigherRank(NomenclaturalCode nomenclaturalCode) {
 331         JTextArea textArea = new JTextArea("Everything below that rank should be imported:");
 332         JScrollPane scrollPane = new JScrollPane(textArea);
 333         textArea.setLineWrap(true);
 334         textArea.setWrapStyleWord(true);
 335         scrollPane.setPreferredSize( new Dimension( 600, 50 ) );
 336
 337         List<Rank> rankList = new ArrayList<Rank>();
 338         rankList = getTermService().list(Rank.class, null, null, null, null);
 339
 340         List<String> rankListStr = new ArrayList<String>();
 341         for (Rank r:rankList) {
 342             rankListStr.add(r.toString());
 343         }
 344         String s = (String)JOptionPane.showInputDialog(
 345                 null,
 346                 scrollPane,
 347                 null,
 348                 JOptionPane.PLAIN_MESSAGE,
 349                 null,
 350                 rankListStr.toArray(),
 351                 "Suprageneric Taxon");
 352
 353         Rank cR = null;
 354         try {
 355             cR = Rank.getRankByEnglishName(s,nomenclaturalCode,true);
 356         } catch (UnknownCdmTypeException e) {
 357             logger.warn("Unknown rank ?!"+s);
 358             logger.warn(e);
 359         }
 360         return cR;
 361     }
 362
 363
 364     @Override
 365     protected boolean isIgnore(TaxonXImportState state) {
 366         return false;
 367     }
 368
 369
 370 }