cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenUserInteraction.java

   1 /**
   2  * Copyright (C) 2013 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 package eu.etaxonomy.cdm.io.specimen;
  10
  11 import java.awt.Color;
  12 import java.awt.Dimension;
  13 import java.awt.event.ItemEvent;
  14 import java.awt.event.ItemListener;
  15 import java.io.Serializable;
  16 import java.util.ArrayList;
  17 import java.util.Collections;
  18 import java.util.HashMap;
  19 import java.util.HashSet;
  20 import java.util.List;
  21 import java.util.Map;
  22 import java.util.Set;
  23 import java.util.UUID;
  24
  25 import javax.swing.BoxLayout;
  26 import javax.swing.ButtonGroup;
  27 import javax.swing.JLabel;
  28 import javax.swing.JOptionPane;
  29 import javax.swing.JPanel;
  30 import javax.swing.JRadioButton;
  31 import javax.swing.JScrollPane;
  32 import javax.swing.JTextArea;
  33
  34 import org.apache.commons.lang.StringUtils;
  35 import org.apache.logging.log4j.LogManager;
  36 import org.apache.logging.log4j.Logger;
  37
  38 import eu.etaxonomy.cdm.api.service.IReferenceService;
  39 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  40 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  41 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  42 import eu.etaxonomy.cdm.model.reference.OriginalSourceBase;
  43 import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
  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.Taxon;
  48 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  49 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  50
  51 /**
  52  * @author pkelbert
  53  * @since 21 juin 2013
  54  */
  55 public class SpecimenUserInteraction implements ItemListener, Serializable {
  56
  57     private static final long serialVersionUID = 6384263183459028523L;
  58     @SuppressWarnings("unused")
  59     private static final Logger log = LogManager.getLogger();
  60
  61     public Classification askForClassification(Map<String, Classification> classMap){
  62         List<String> possibilities = new ArrayList<String>(classMap.keySet());
  63         Collections.sort(possibilities);
  64
  65         if (classMap.keySet().size()>0) {
  66             classMap.put("Nothing matches, create a new classification",null);
  67             possibilities.add(0, "Nothing matches, create a new classification");
  68         } else {
  69             return null;
  70         }
  71
  72         JTextArea textArea = new JTextArea("Which existing classification should be used ?");
  73         JScrollPane scrollPane = new JScrollPane(textArea);
  74         textArea.setLineWrap(true);
  75         textArea.setWrapStyleWord(true);
  76         scrollPane.setPreferredSize( new Dimension( 500, 50 ) );
  77
  78         String s = null;
  79         while (s == null) {
  80             s= (String)JOptionPane.showInputDialog(
  81                     null,
  82                     scrollPane,
  83                     "Please select a classification in the list",
  84                     JOptionPane.PLAIN_MESSAGE,
  85                     null,
  86                     possibilities.toArray(),
  87                     "Nothing matches, create a new classification");
  88         }
  89         return classMap.get(s);
  90     }
  91
  92     /**
  93      * @return the name for the new Classification
  94      */
  95     public String createNewClassification() {
  96         JTextArea textArea = new JTextArea("How should the classification be named ?");
  97         JScrollPane scrollPane = new JScrollPane(textArea);
  98         textArea.setLineWrap(true);
  99         textArea.setWrapStyleWord(true);
 100         scrollPane.setPreferredSize( new Dimension( 500, 50 ) );
 101
 102         String s = null;
 103         while (s == null) {
 104             s=(String)JOptionPane.showInputDialog(
 105                     null,
 106                     scrollPane,
 107                     "Get full classification name",
 108                     JOptionPane.PLAIN_MESSAGE,
 109                     null,
 110                     null,
 111                     "ABCD Import");
 112         }
 113         return s;
 114     }
 115
 116     /**
 117      * @param refMap
 118      * @return
 119      */
 120     public Reference askForReference(Map<String, Reference> refMap) {
 121         List<String>  possibilities = new ArrayList<>(refMap.keySet());
 122         Collections.sort(possibilities);
 123         if (refMap.keySet().size()>0) {
 124             refMap.put("Nothing matches, create a new reference",null);
 125             possibilities.add(0, "Nothing matches, create a new reference");
 126         } else {
 127             return null;
 128         }
 129
 130         JTextArea textArea = new JTextArea("Which existing reference should be used?");
 131         JScrollPane scrollPane = new JScrollPane(textArea);
 132         textArea.setLineWrap(true);
 133         textArea.setWrapStyleWord(true);
 134         scrollPane.setPreferredSize( new Dimension( 700, 50 ) );
 135
 136         String s = null;
 137         while (s == null) {
 138             s= (String)JOptionPane.showInputDialog(
 139                     null,
 140                     scrollPane,
 141                     "Please select a reference in the list",
 142                     JOptionPane.PLAIN_MESSAGE,
 143                     null,
 144                     possibilities.toArray(),
 145                     "ABCD reference");
 146         }
 147         return refMap.get(s);
 148     }
 149
 150     /**
 151      * @param refMap
 152      * @param iReferenceService
 153      * @param docSources
 154      * @return
 155      */
 156     public List<OriginalSourceBase> askForSource(Map<String, OriginalSourceBase> refMap, String currentElement, String blabla,
 157             IReferenceService iReferenceService, List<String> docSources) {
 158
 159 //        System.out.println(refMap);
 160         List<String>  possibilities = new ArrayList<> (refMap.keySet());
 161
 162         Set<String> all = new HashSet<>();
 163         all.addAll(possibilities);
 164
 165         List<String> allList = new ArrayList<String>();
 166         allList.addAll(all);
 167         Collections.sort(allList);
 168         allList.add(0, "Create a new source");
 169
 170         JLabel label = new JLabel(blabla);
 171
 172         sources=new ArrayList<String>();
 173
 174         JPanel checkPanel = null;
 175         ButtonGroup group = null;
 176         JScrollPane scrollPane = null;
 177
 178         JRadioButton jcb = null;
 179
 180         Object[] options = {"Add and close", "Add and continue - I want to add more sources","Close without adding anything"};
 181
 182 //        System.out.println(docSources);
 183         int n=1;
 184         while (n==1){
 185             group = new ButtonGroup();
 186             checkPanel = new JPanel();
 187             checkPanel.setLayout(new BoxLayout(checkPanel, BoxLayout.Y_AXIS));
 188 //            allList.removeAll(sources);
 189             scrollPane = new JScrollPane(checkPanel);
 190             scrollPane.setPreferredSize( new Dimension( 700, 300 ) );
 191
 192             checkPanel.add(label);
 193
 194             for (String ch:allList){
 195                 if (StringUtils.isBlank(ch)) {
 196                     continue;
 197                 }
 198 //                System.out.println("HOP ="+ch+"=");
 199                 if(docSources.contains(ch)) {
 200                     jcb = new JRadioButton("<html>"+ch.replace("---", "<br/>")+"</html>");
 201                     jcb.setForeground(Color.blue);
 202                 } else {
 203                     jcb = new JRadioButton("<html>"+ch.replace("---", "<br/>")+"</html>");
 204                     jcb.setForeground(Color.black);
 205                 }
 206                 jcb.addItemListener(this);
 207                 group.add(jcb);
 208                 checkPanel.add(jcb);
 209             }
 210
 211             n = JOptionPane.showOptionDialog(null,
 212                     scrollPane,
 213                     "Choose a source for "+currentElement +"(in blue the source from the document)",
 214                     JOptionPane.YES_NO_CANCEL_OPTION,
 215                     JOptionPane.QUESTION_MESSAGE,
 216                     null,
 217                     options,
 218                     options[1]);
 219             if(n<3 && !currentSource.isEmpty() && !currentSource.equalsIgnoreCase("Create a new source")) {
 220                 sources.add(currentSource);
 221             }
 222 //            System.out.println("current source: "+currentSource);
 223             if(currentSource.equalsIgnoreCase("Create a new source")){
 224                 String a = createNewSource();
 225                 if (a!=null && !a.isEmpty()) {
 226                     sources.add(a);
 227                 }
 228             }
 229         }
 230
 231         List<OriginalSourceBase> dess = new ArrayList<>();
 232         for (String src:sources){
 233             if (refMap.get(src) !=null) {
 234                 dess.add(refMap.get(src));
 235             }
 236             else{
 237                 Reference re = null;
 238                 String titlecache="";
 239                 String micro="";
 240                 if (src.indexOf("---")>-1){
 241                     titlecache = src.split("---")[0].trim();
 242                     micro=src.split("---")[1].trim();
 243                 }
 244                 else{
 245                     titlecache= src.split("---")[0].trim();
 246                 }
 247
 248                 List<Reference> references = iReferenceService.list(Reference.class, null, null, null, null);
 249                 for (Reference reference:references){
 250                     if (reference.getTitleCache().equalsIgnoreCase(titlecache)) {
 251                         re=reference;
 252                     }
 253                 }
 254                 if(re == null){
 255                     re = ReferenceFactory.newGeneric();
 256                     re.setTitleCache(titlecache);
 257                     iReferenceService.saveOrUpdate(re);
 258                 }
 259
 260                 dess.add(IdentifiableSource.NewInstance(OriginalSourceType.Import,null, null, re,micro));
 261             }
 262         }
 263         return dess;
 264     }
 265
 266     public String createNewReference() {
 267         JTextArea textArea = new JTextArea("How should the reference be named ?");
 268         JScrollPane scrollPane = new JScrollPane(textArea);
 269         textArea.setLineWrap(true);
 270         textArea.setWrapStyleWord(true);
 271         scrollPane.setPreferredSize( new Dimension( 500, 50 ) );
 272
 273         String s = null;
 274         while (s == null) {
 275             s= (String)JOptionPane.showInputDialog(
 276                     null,
 277                     scrollPane,
 278                     "Get full reference name",
 279                     JOptionPane.PLAIN_MESSAGE,
 280                     null,
 281                     null,
 282                     "ABCD Import from XML");
 283         }
 284         return s;
 285     }
 286
 287     public String createNewSource() {
 288         JTextArea textArea = new JTextArea("How should the source be named? If there is a citation detail, prefix it with 3 minus signs ('---').");
 289         JScrollPane scrollPane = new JScrollPane(textArea);
 290         textArea.setLineWrap(true);
 291         textArea.setWrapStyleWord(true);
 292         scrollPane.setPreferredSize( new Dimension( 500, 50 ) );
 293
 294         String s = null;
 295         while (s == null) {
 296             s= (String)JOptionPane.showInputDialog(
 297                     null,
 298                     scrollPane,
 299                     "Get full source name",
 300                     JOptionPane.PLAIN_MESSAGE,
 301                     null,
 302                     null,
 303                     "ABCD Import from XML");
 304         }
 305         return s;
 306     }
 307
 308     public TaxonDescription askForDescriptionGroup(Set<TaxonDescription> descriptions) {
 309         JTextArea textArea = new JTextArea("One or several description group(s) does already exist for this taxon.");
 310         JScrollPane scrollPane = new JScrollPane(textArea);
 311         textArea.setLineWrap(true);
 312         textArea.setWrapStyleWord(true);
 313         scrollPane.setPreferredSize( new Dimension( 700, 50 ) );
 314
 315         Map<String,TaxonDescription> descrMap = new HashMap<String, TaxonDescription>();
 316
 317         int descCnt=1;
 318         for (TaxonDescription description : descriptions){
 319 //            System.out.println("descr. titlecache "+description.getTitleCache());
 320             Set<IdentifiableSource> sources =  description.getTaxon().getSources();
 321             sources.addAll(description.getSources());
 322             List<String> src=new ArrayList<String>();
 323             for (IdentifiableSource s:sources) {
 324                 src.add(s.getCitation().getTitleCache());
 325             }
 326             List<String> srcb = new ArrayList<String>(new HashSet<>(src));
 327             if (srcb.size()>0) {
 328                 if(descrMap.containsKey(descCnt+": "+description.getTitleCache()+"("+StringUtils.join(srcb,";")+")")) {
 329                     descCnt+=1;
 330                 }
 331                 descrMap.put(descCnt+": "+description.getTitleCache()+"("+StringUtils.join(srcb,";")+")",description);
 332             }
 333             else {
 334                 if(descrMap.containsKey(description.getTitleCache())) {
 335                     descCnt+=1;
 336                 }
 337                 descrMap.put(descCnt+": "+description.getTitleCache(),description);
 338                 //            for (IdentifiableSource source:sources){
 339                 //                if(ref.equals(source.getCitation())) {
 340                 //                    taxonDescription = description;
 341                 //                }
 342                 //            }
 343             }
 344         }
 345         List<String>  possibilities = new ArrayList<>(descrMap.keySet());
 346         if (possibilities.size()==0) {
 347             return null;
 348         }
 349         Collections.sort(possibilities);
 350
 351         descrMap.put("No, add a brand new description group", null);
 352         possibilities.add(0, "No, add a brand new description group");
 353
 354         String s = null;
 355         while (s == null) {
 356             s= (String)JOptionPane.showInputDialog(
 357                     null,
 358                     scrollPane,
 359                     "What should be done? Should an existing group be reused ? ",
 360                     JOptionPane.PLAIN_MESSAGE,
 361                     null,
 362                     possibilities.toArray(),
 363                     "No, add a brand new description group");
 364         }
 365
 366         if (descrMap.get(s) !=null) {
 367             return descrMap.get(s);
 368         } else {
 369             return null;
 370         }
 371     }
 372
 373     /**
 374      * Look if the same name already exists in the ALL classifications and ask the user to select one or none.
 375      * @param scientificName
 376      * @param taxonList
 377      * @return null if not found, or the selected Taxon
 378      */
 379     @SuppressWarnings("rawtypes")
 380     public Taxon askWhereToFixData(String scientificName, List<TaxonBase> taxonList, Classification classification) {
 381         Map<String,TaxonNode> classMap = new HashMap<>();
 382         boolean sameClassification=false;
 383         Taxon n = null;
 384         for (TaxonBase taxonBase: taxonList){
 385             if(taxonBase.isInstanceOf(Taxon.class)){
 386                 Taxon taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
 387                 for (TaxonNode node : taxon.getTaxonNodes()){
 388                     classMap.put("Reuse the one from the classification \""+node.getClassification().getTitleCache()+"\"", node);
 389                     if (node.getClassification().getUuid().equals(classification.getUuid())) {
 390                         sameClassification=true;
 391                         n=node.getTaxon();
 392                     }
 393                 }
 394             }
 395         }
 396         if (classMap.keySet().size()==1 && sameClassification) {
 397             return n;
 398         }
 399
 400         JTextArea textArea = new JTextArea("The same taxon ("+scientificName+") already exists in an other classification.");
 401         JScrollPane scrollPane = new JScrollPane(textArea);
 402         textArea.setLineWrap(true);
 403         textArea.setWrapStyleWord(true);
 404         scrollPane.setPreferredSize( new Dimension( 700, 50 ) );
 405
 406         List<String>  possibilities = new ArrayList<String> (classMap.keySet());
 407         if (possibilities.size()==0) {
 408             return null;
 409         }
 410         Collections.sort(possibilities);
 411         if(!sameClassification){
 412             classMap.put("Add a brand new Taxon to the current classification, no recycling please", null);
 413             possibilities.add(0, "Add a brand new Taxon to the current classification, no recycling please");
 414         }
 415         String s = null;
 416         while (s == null) {
 417             s= (String)JOptionPane.showInputDialog(
 418                     null,
 419                     scrollPane,
 420                     "What should be done? ",
 421                     JOptionPane.PLAIN_MESSAGE,
 422                     null,
 423                     possibilities.toArray(),
 424                     "Add a brand new Taxon to the current classification, no recycling please");
 425         }
 426
 427         if (classMap.get(s) !=null) {
 428             return classMap.get(s).getTaxon();
 429         } else {
 430             return null;
 431         }
 432     }
 433
 434     /**
 435      * Look if the same TaxonBase already exists in the SAME classification
 436      * @param taxonBaseList
 437      * @return null if not found, or the corresponding Taxon
 438      */
 439     @SuppressWarnings("rawtypes")
 440     public Taxon lookForTaxaIntoCurrentClassification(List<TaxonBase> taxonBaseList, Classification classification) {
 441         Taxon taxonFound =null;
 442         for (TaxonBase taxonBase:taxonBaseList){
 443             if(taxonBase.isInstanceOf(Taxon.class)){
 444                 Taxon taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
 445                 for (TaxonNode node : taxon.getTaxonNodes()){
 446                     UUID classUuid = node.getClassification().getUuid();
 447                     if (classification.getUuid().equals(classUuid)){
 448                         taxonFound=taxon;
 449                     }
 450                 }
 451             }
 452         }
 453         return taxonFound;
 454     }
 455
 456     List<String> sources = new ArrayList<>();
 457     String currentSource = "";
 458
 459     @Override
 460     public void itemStateChanged(ItemEvent e) {
 461         JRadioButton cb = (JRadioButton) e.getItem();
 462         int state = e.getStateChange();
 463         if (state == ItemEvent.SELECTED) {
 464             currentSource=cb.getText().replace("</html>", "").replace("<html>","")
 465                     .replace("<br/>","---").replace("<font color=\"blue\">","").replace("</font>","");
 466         } else {
 467             currentSource="";
 468         }
 469     }
 470 }