cdmlib-model/src/main/java/eu/etaxonomy/cdm/format/ReferencingObjectFormatter.java

   1 /**
   2 * Copyright (C) 2021 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.format;
  10
  11 import java.lang.reflect.InvocationTargetException;
  12 import java.lang.reflect.Method;
  13 import java.util.Set;
  14
  15 import org.apache.commons.lang3.StringUtils;
  16
  17 import eu.etaxonomy.cdm.common.CdmUtils;
  18 import eu.etaxonomy.cdm.format.occurrences.DistanceStringFormatter;
  19 import eu.etaxonomy.cdm.model.agent.AgentBase;
  20 import eu.etaxonomy.cdm.model.common.CdmBase;
  21 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  22 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  23 import eu.etaxonomy.cdm.model.common.Language;
  24 import eu.etaxonomy.cdm.model.common.LanguageString;
  25 import eu.etaxonomy.cdm.model.common.LanguageStringBase;
  26 import eu.etaxonomy.cdm.model.common.Marker;
  27 import eu.etaxonomy.cdm.model.common.MarkerType;
  28 import eu.etaxonomy.cdm.model.common.RelationshipBase;
  29 import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
  30 import eu.etaxonomy.cdm.model.common.TimePeriod;
  31 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  32 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  33 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  34 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  35 import eu.etaxonomy.cdm.model.description.Distribution;
  36 import eu.etaxonomy.cdm.model.description.IDescribable;
  37 import eu.etaxonomy.cdm.model.description.KeyStatement;
  38 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  39 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  40 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  41 import eu.etaxonomy.cdm.model.description.TaxonInteraction;
  42 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
  43 import eu.etaxonomy.cdm.model.description.TextData;
  44 import eu.etaxonomy.cdm.model.location.NamedArea;
  45 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  46 import eu.etaxonomy.cdm.model.name.HybridRelationship;
  47 import eu.etaxonomy.cdm.model.name.NameRelationship;
  48 import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
  49 import eu.etaxonomy.cdm.model.name.NomenclaturalSource;
  50 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  51 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  52 import eu.etaxonomy.cdm.model.name.TaxonName;
  53 import eu.etaxonomy.cdm.model.name.TextualTypeDesignation;
  54 import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
  55 import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
  56 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  57 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  58 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  59 import eu.etaxonomy.cdm.model.permission.Group;
  60 import eu.etaxonomy.cdm.model.permission.User;
  61 import eu.etaxonomy.cdm.model.reference.NamedSource;
  62 import eu.etaxonomy.cdm.model.reference.OriginalSourceBase;
  63 import eu.etaxonomy.cdm.model.taxon.Classification;
  64 import eu.etaxonomy.cdm.model.taxon.SecundumSource;
  65 import eu.etaxonomy.cdm.model.taxon.Taxon;
  66 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  67 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  68 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  69 import eu.etaxonomy.cdm.model.term.Representation;
  70
  71 /**
  72  * @author a.mueller
  73  * @date 19.03.2021
  74  */
  75 public class ReferencingObjectFormatter {
  76
  77
  78     public static String format(CdmBase element, Language defaultLanguage) {
  79         return format(element, null, defaultLanguage);
  80     }
  81
  82
  83     public static String format(CdmBase element, String target, Language defaultLanguage) {
  84
  85         String resultString = null;
  86         if (element == null){
  87             return null;
  88         }else if (element instanceof IdentifiableEntity) {
  89             resultString = ((IdentifiableEntity<?>) element).getTitleCache();
  90         }else if (element instanceof OriginalSourceBase) {
  91             OriginalSourceBase originalSource = (OriginalSourceBase) element;
  92 //              ISourceable sourcedObject = originalSource.getSourcedObj();
  93             //due to #5743 the bidirectionality for sourced object had to be removed
  94
  95             String sourceObjectTitle = "sourced object data not available (#5743)";
  96
  97             //it is now possible for NomenclaturalSource as they link to the sourced name
  98             if (originalSource instanceof NomenclaturalSource){
  99                 TaxonName sourcedName = ((NomenclaturalSource)originalSource).getSourcedName();
 100                 sourceObjectTitle = sourcedName == null ? "Source orphaned, not attached to a name" :
 101                     "for " + sourcedName.getTitleCache();
 102             }else if (originalSource instanceof SecundumSource){
 103                 TaxonBase<?> sourcedTaxon = ((SecundumSource)originalSource).getSourcedTaxon();
 104                 sourceObjectTitle = sourcedTaxon == null ? "Source orphaned, not attached to a taxon" :
 105                     "for " + sourcedTaxon.getTitleCache();
 106             }else if (originalSource instanceof DescriptionElementSource){
 107                 sourceObjectTitle = getCache((DescriptionElementSource)originalSource, defaultLanguage);
 108             }else if (originalSource instanceof IdentifiableSource && isNotBlank(target) ){
 109                 sourceObjectTitle = "for " + target;
 110             }else if (originalSource instanceof NamedSource && isNotBlank(target) ){
 111                 sourceObjectTitle = "for " + target;
 112             }
 113             resultString = CdmUtils.concat("; ", new String[]{originalSource.getIdNamespace(), originalSource.getIdInSource(), sourceObjectTitle});
 114         }else if (element instanceof LanguageStringBase) {
 115             resultString = ((LanguageStringBase) element).getText();
 116         }else if (element instanceof DescriptionElementBase) {
 117             resultString = getCache((DescriptionElementBase) element, defaultLanguage);
 118         }else if (element instanceof RelationshipBase<?, ?, ?>) {
 119             resultString = getCache((RelationshipBase<?, ?, ?>) element, defaultLanguage);
 120         }else if (element instanceof TypeDesignationBase<?>) {
 121             resultString = getCache((TypeDesignationBase<?>) element, defaultLanguage);
 122         }else if (element instanceof HomotypicalGroup) {
 123             resultString = getCache((HomotypicalGroup) element);
 124         }else if (element instanceof TaxonNode) {
 125             resultString = getCache((TaxonNode) element);
 126         }else if (element instanceof DeterminationEvent) {
 127             resultString = getCache((DeterminationEvent) element);
 128         }else if (element instanceof NomenclaturalStatus) {
 129             resultString = getCache((NomenclaturalStatus) element);
 130         }else if (element instanceof GatheringEvent){
 131             resultString = getCache((GatheringEvent) element);
 132         }else if (element instanceof Marker) {
 133             Marker marker = (Marker) element;
 134             MarkerType type = marker.getMarkerType();
 135             resultString = (type == null ? "- no marker type -" : marker.getMarkerType().getLabel()) + " (" + marker.getFlag() + ")";
 136         }else if (element instanceof User) {
 137             User user = (User) element;
 138             resultString = user.getUsername();
 139         }else if (element instanceof Group) {
 140             Group group = (Group) element;
 141             resultString = group.getName();
 142         }else if (element instanceof KeyStatement) {
 143             KeyStatement keyStatement = (KeyStatement) element;
 144             resultString = getCache(keyStatement);
 145         }else{
 146             // TODO write return texts for HomotypicalGroup, etc.
 147             resultString = element.toString();
 148         }
 149
 150         if (resultString == null){
 151             resultString = element.toString();
 152         }
 153         return resultString;
 154     }
 155
 156     private static String getCache(DescriptionElementSource source, Language defaultLanguage) {
 157         DescriptionElementBase sourcedElement = source.getSourcedElement();
 158
 159         if (sourcedElement == null){
 160             return "Source orphaned, not attached to a fact";
 161         }
 162         String superLabel = getDescribedObjectLabel(sourcedElement.getInDescription());
 163         String result = CdmUtils.concat(": ", DescriptionElementFormatter.format(sourcedElement, defaultLanguage), superLabel);
 164         return result;
 165     }
 166
 167     private static String getDescribedObjectLabel(DescriptionBase<?> inDescription) {
 168         IDescribable<?> entity = inDescription.describedEntity();
 169         if (entity != null){
 170             return entity.getTitleCache();
 171         }else{
 172             return inDescription.getTitleCache();
 173         }
 174     }
 175
 176     private static String getCache(RelationshipBase<?, ?, ?> rel, Language defaultLanguage) {
 177         rel = CdmBase.deproxy(rel);
 178         RelationshipTermBase<?> type = rel.getType();
 179         IdentifiableEntity<?> from;
 180         IdentifiableEntity<?> to;
 181         if (rel.isInstanceOf(NameRelationship.class)){
 182             from = ((NameRelationship)rel).getFromName();
 183             to = ((NameRelationship)rel).getToName();
 184         }else if (rel.isInstanceOf(HybridRelationship.class)){
 185             from = ((HybridRelationship)rel).getParentName();
 186             to = ((HybridRelationship)rel).getHybridName();
 187         }else if (rel.isInstanceOf(TaxonRelationship.class)){
 188             from = ((TaxonRelationship)rel).getFromTaxon();
 189             to = ((TaxonRelationship)rel).getToTaxon();
 190         }else{
 191             try {
 192                 Method fromMethod = rel.getClass().getMethod("getRelatedFrom");
 193                 Method toMethod = rel.getClass().getMethod("getRelatedFrom");
 194                 fromMethod.setAccessible(true);
 195                 toMethod.setAccessible(true);
 196                 from = (IdentifiableEntity<?>)fromMethod.invoke(rel);
 197                 to = (IdentifiableEntity<?>)toMethod.invoke(rel);
 198             } catch (NoSuchMethodException | SecurityException | IllegalAccessException
 199                 | IllegalArgumentException | InvocationTargetException e) {
 200                 throw new RuntimeException(e);
 201             }
 202         }
 203         String typeLabel = null;
 204         if (type != null){
 205             Representation typeRepr = type.getPreferredRepresentation(defaultLanguage);
 206             if (typeRepr != null){
 207                 typeLabel = typeRepr.getAbbreviatedLabel();
 208             }
 209             if (isBlank(typeLabel) && typeRepr != null){
 210                 typeLabel = typeRepr.getLabel();
 211             }
 212             if (isBlank(typeLabel) ){
 213                 typeLabel = type.getSymbol();
 214             }
 215             if (isBlank(typeLabel)){
 216                 typeLabel = type.getTitleCache();
 217             }
 218         }
 219         if (isBlank(typeLabel)){
 220             typeLabel = "->";
 221         }
 222         String result = CdmUtils.concat(" ", new String[]{from == null ? null : from.getTitleCache(),
 223                 typeLabel, to == null? null : to.getTitleCache()});
 224         return result;
 225     }
 226
 227     private static String getCache(GatheringEvent gatheringEvent){
 228         String ALTITUDE_PREFIX = "alt. ";
 229         final String METER = "m";
 230
 231         String result = "";
 232
 233         //collector
 234         AgentBase<?> collector = CdmBase.deproxy(gatheringEvent.getCollector());
 235         String collectorStr = collector == null? null : collector.getTitleCache();
 236         result = CdmUtils.concat(", ", result, collectorStr);
 237
 238         //gathering period
 239         TimePeriod gatheringPeriod = gatheringEvent.getTimeperiod();
 240         result = CdmUtils.concat(", ", result, (gatheringPeriod == null? null : gatheringPeriod.toString()));
 241
 242         //country
 243         String strCountry = null;
 244         NamedArea country = gatheringEvent.getCountry();
 245         Representation repCountry = country == null ? null : country.getRepresentation(Language.DEFAULT());
 246         strCountry = repCountry == null ? null: repCountry.getLabel();
 247         result = CdmUtils.concat(", ", result, strCountry);
 248
 249         //locality
 250         LanguageString locality = gatheringEvent.getLocality();
 251         if (locality != null) {
 252             result = CdmUtils.concat(", ", result, locality.getText());
 253         }
 254
 255         //elevation
 256         String elevationStr;
 257         if (isNotBlank(gatheringEvent.getAbsoluteElevationText())){
 258             elevationStr = gatheringEvent.getAbsoluteElevationText();
 259         }else{
 260             String text = gatheringEvent.getAbsoluteElevationText();
 261             Integer min = gatheringEvent.getAbsoluteElevation();
 262             Integer max = gatheringEvent.getAbsoluteElevationMax();
 263             elevationStr = DistanceStringFormatter.distanceString(min, max, text, METER);
 264         }
 265         if (isNotBlank(elevationStr)){
 266             result = CdmUtils.concat(", " , result, ALTITUDE_PREFIX);
 267             result += elevationStr;
 268         }
 269
 270         //exact locality
 271         if (gatheringEvent.getExactLocation() != null){
 272             String exactLocation = gatheringEvent.getExactLocation().toSexagesimalString(false, false);
 273             result = CdmUtils.concat(", ", result, exactLocation);
 274         }
 275
 276         return result;
 277     }
 278
 279     private static String getCache(DeterminationEvent detEvent) {
 280         //taxon
 281         String taxonStr = null;
 282         TaxonName taxonName = detEvent.getTaxonName();
 283         TaxonBase<?> taxon = detEvent.getTaxon();
 284         if (taxonName != null){
 285             taxonStr = taxonName.getTitleCache();
 286         }
 287         if (isBlank(taxonStr) && taxon != null){
 288             taxonStr = taxon.getTitleCache();
 289         }
 290         if (isBlank(taxonStr)){
 291             taxonStr = "no or unlabled taxon";
 292         }
 293
 294         //unit
 295         SpecimenOrObservationBase<?> unit = detEvent.getIdentifiedUnit();
 296         String unitStr;
 297         if (unit != null){
 298             unitStr = unit.getTitleCache();
 299             if (isBlank(unitStr)){
 300                 unitStr = "Unlabled unit";
 301             }
 302         }else{
 303             unitStr = "no unit";
 304         }
 305
 306         String result = CdmUtils.concat(" determined as ", unitStr, taxonStr);
 307
 308         return result;
 309     }
 310
 311     private static String getCache(TaxonNode taxonNode) {
 312         String result = "";
 313         Classification classification = taxonNode.getClassification();
 314         if (classification != null){
 315             String classificationStr = classification.getName() == null ? "" : classification.getName().getText();
 316             result = CdmUtils.concat("" , result, classificationStr);
 317             if (isBlank(result)){
 318                 result = classification.toString();
 319             }
 320         }
 321         String parentStr;
 322         TaxonNode parentNode = taxonNode.getParent();
 323         if (parentNode == null){
 324             parentStr = "no parent";
 325         }else{
 326             Taxon parentTaxon = parentNode.getTaxon();
 327             if (parentTaxon == null){
 328                 parentStr = "no parent taxon";
 329             }else{
 330                 TaxonName parentName = parentTaxon.getName();
 331                 if (parentName == null){
 332                     parentStr = "child of " + parentTaxon.getTitleCache();
 333                 }else{
 334                     parentStr = "child of " + parentName.getTitleCache();
 335                 }
 336             }
 337         }
 338         result = CdmUtils.concat(": ", result, parentStr);
 339
 340         return result;
 341     }
 342
 343     private static String getCache(TypeDesignationBase<?> designation, Language defaultLanguage) {
 344         designation = CdmBase.deproxy(designation);
 345         //from
 346         String fromString = null;
 347         Set<TaxonName> from = designation.getTypifiedNames();
 348         if(from != null){
 349             for (TaxonName name : from){
 350                 fromString = CdmUtils.concat(",", fromString, name.getTitleCache());
 351             }
 352         }
 353         //to
 354         IdentifiableEntity<?> to = null;
 355         String toStr = "";
 356         if (designation.isInstanceOf(SpecimenTypeDesignation.class)){
 357             to = ((SpecimenTypeDesignation)designation).getTypeSpecimen();
 358         }else if (designation.isInstanceOf(NameTypeDesignation.class)){
 359             to = ((NameTypeDesignation)designation).getTypeName();
 360         }else if (designation.isInstanceOf(TextualTypeDesignation.class)){
 361             toStr = ((TextualTypeDesignation)designation).getPreferredText(defaultLanguage);
 362         }else{
 363             throw new RuntimeException("Type Designation class not supported: " +  designation.getClass().getName());
 364         }
 365         toStr = to == null? toStr : to.getTitleCache();
 366         //status
 367         String typeLabel = null;
 368         TypeDesignationStatusBase<?> status = designation.getTypeStatus();
 369         if (status != null){
 370             Representation typeRepr = status.getPreferredRepresentation(defaultLanguage);
 371             if (typeRepr != null){
 372                 typeLabel = typeRepr.getAbbreviatedLabel();
 373             }
 374             if (isBlank(typeLabel) && typeRepr != null){
 375                 typeLabel = typeRepr.getLabel();
 376             }
 377             if (isBlank(typeLabel) ){
 378                 typeLabel = status.getSymbol();
 379             }
 380             if (isBlank(typeLabel)){
 381                 typeLabel = status.getTitleCache();
 382             }
 383         }
 384         if (isBlank(typeLabel)){
 385             typeLabel = "->";
 386         }
 387         //concat
 388         String result = CdmUtils.concat(" ", new String[]{fromString, typeLabel, toStr});
 389         return result;
 390     }
 391
 392     private static String getCache(HomotypicalGroup hg) {
 393         String result = "";
 394         for (TaxonName tnb : hg.getTypifiedNames()){
 395             result = CdmUtils.concat(", ", result, tnb.getTitleCache());
 396         }
 397         if (isBlank(result)){
 398             result = "No typified names";
 399         }
 400         return result;
 401     }
 402
 403     private static String getCache(KeyStatement ks) {
 404         String result = "";
 405         LanguageString ls = ks.getPreferredLanguageString(Language.DEFAULT());
 406         if (ls != null && CdmUtils.isNotBlank(ls.getText())){
 407             result = ls.getText();
 408         }else{
 409             result = ks.toString();
 410         }
 411         return result;
 412     }
 413
 414     private static String getCache(NomenclaturalStatus nomStatus) {
 415         String result = nomStatus.getName().getTitleCache();
 416         if (nomStatus.getType()!= null){
 417             Representation rep = nomStatus.getType().getPreferredRepresentation(Language.DEFAULT());
 418             if (rep != null){
 419                 result = CdmUtils.concat(": ", rep.getAbbreviatedLabel(), result);
 420             }
 421         }
 422         return result;
 423     }
 424
 425
 426     private static boolean isNotBlank(String str){
 427         return StringUtils.isNotBlank(str);
 428     }
 429
 430     private static boolean isBlank(String str){
 431         return StringUtils.isBlank(str);
 432     }
 433
 434     //from taxeditor DescriptionHelper
 435     private static String getCache(DescriptionElementBase element,
 436             Language defaultLanguage) {
 437
 438         String mainElementLabel= null;
 439         DescriptionBase<?> descr = element.getInDescription();
 440         descr = CdmBase.deproxy(descr);
 441
 442         if (descr != null){
 443             if (descr.isInstanceOf(TaxonDescription.class)){
 444                 Taxon taxon = CdmBase.deproxy(descr, TaxonDescription.class).getTaxon();
 445                 if (taxon != null){
 446                     mainElementLabel = taxon.getTitleCache();
 447                 }
 448             }else if (descr.isInstanceOf(SpecimenDescription.class)){
 449                 SpecimenOrObservationBase<?> specimen = CdmBase.deproxy(descr, SpecimenDescription.class).getDescribedSpecimenOrObservation();
 450                 if (specimen != null){
 451                     mainElementLabel = specimen.getTitleCache();
 452                 }
 453             }else if (descr.isInstanceOf(TaxonNameDescription.class)){
 454                 TaxonName name = CdmBase.deproxy(descr, TaxonNameDescription.class).getTaxonName();
 455                 if (name != null){
 456                     mainElementLabel = name.getTitleCache();
 457                 }
 458             }
 459         }
 460
 461         String cache = null;
 462         if (element instanceof TextData) {
 463             //cache = ((TextData) element).getText(language);
 464             cache = "Text Data";
 465         }
 466         if (element instanceof CommonTaxonName) {
 467             cache = ((CommonTaxonName) element).getName();
 468         }
 469         if (element instanceof TaxonInteraction) {
 470             Taxon taxon2 = ((TaxonInteraction) element).getTaxon2();
 471             if(taxon2 != null && taxon2.getName() != null){
 472                 cache = taxon2.getName().getTitleCache();
 473             }else{
 474                 cache = "No taxon chosen";
 475             }
 476         }
 477         if (element instanceof Distribution) {
 478             Distribution distribution = (Distribution) element;
 479
 480             NamedArea area = distribution.getArea();
 481             if(area != null){
 482                 cache =  area.getLabel();
 483
 484                 PresenceAbsenceTerm status = distribution.getStatus();
 485                 if (status == null){
 486                     cache += ", no status";
 487                 }else {
 488                     cache += ", " + status.getLabel();
 489                 }
 490             }
 491         }
 492         String result = cache == null ? "" : cache;
 493         if (isNotBlank(mainElementLabel)){
 494             result = CdmUtils.concat(" ", result, "(" + mainElementLabel + ")");
 495         }
 496         return result;
 497     }
 498
 499 }