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[cdmlib.git] / cdmlib-io / src / main / java / eu / etaxonomy / cdm / io / cdmLight / CdmLightClassificationExport.java
diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightClassificationExport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightClassificationExport.java
index 5c18b30c4ccd9b295e5043d52b0158325f45650a..2f19184b9024b03b450a73f7d2fb501ca2c07dd0 100755 (executable)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightClassificationExport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightClassificationExport.java
@@ -25,7 +25,7 @@ import org.apache.commons.lang3.StringUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
-import eu.etaxonomy.cdm.api.service.dto.CondensedDistribution;
+import eu.etaxonomy.cdm.api.service.geo.IDistributionService;
 import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetComparator;
 import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetContainer;
 import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetFormatter;
@@ -33,8 +33,10 @@ import eu.etaxonomy.cdm.common.CdmUtils;
 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
 import eu.etaxonomy.cdm.compare.name.TypeComparator;
 import eu.etaxonomy.cdm.compare.taxon.HomotypicGroupTaxonComparator;
-import eu.etaxonomy.cdm.ext.geo.IEditGeoService;
 import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
+import eu.etaxonomy.cdm.format.description.CategoricalDataFormatter;
+import eu.etaxonomy.cdm.format.description.QuantitativeDataFormatter;
+import eu.etaxonomy.cdm.format.description.distribution.CondensedDistribution;
 import eu.etaxonomy.cdm.format.reference.OriginalSourceFormatter;
 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
 import eu.etaxonomy.cdm.io.common.CdmExportBase;
@@ -56,6 +58,7 @@ import eu.etaxonomy.cdm.model.common.IdentifiableSource;
 import eu.etaxonomy.cdm.model.common.Identifier;
 import eu.etaxonomy.cdm.model.common.Language;
 import eu.etaxonomy.cdm.model.common.LanguageString;
+import eu.etaxonomy.cdm.model.description.CategoricalData;
 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
 import eu.etaxonomy.cdm.model.description.DescriptionBase;
 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
@@ -63,6 +66,7 @@ import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
 import eu.etaxonomy.cdm.model.description.Distribution;
 import eu.etaxonomy.cdm.model.description.Feature;
 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
+import eu.etaxonomy.cdm.model.description.QuantitativeData;
 import eu.etaxonomy.cdm.model.description.TaxonDescription;
 import eu.etaxonomy.cdm.model.description.TaxonInteraction;
 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
@@ -98,7 +102,8 @@ import eu.etaxonomy.cdm.model.taxon.Taxon;
 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
-import eu.etaxonomy.cdm.model.term.DefinedTerm;
+import eu.etaxonomy.cdm.model.term.IdentifierType;
+import eu.etaxonomy.cdm.model.term.TermTree;
 import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
 import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDtoByRankAndNameComparator;
 import eu.etaxonomy.cdm.strategy.cache.HTMLTagRules;
@@ -107,6 +112,8 @@ import eu.etaxonomy.cdm.strategy.cache.TaggedText;
 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
 
 /**
+ * The export exporting a classification or a taxonomic subtree into CDM light.
+ *
  * @author k.luther
  * @since 15.03.2017
  */
@@ -117,7 +124,7 @@ public class CdmLightClassificationExport
     private static final long serialVersionUID = 2518643632756927053L;
 
     @Autowired
-    private IEditGeoService geoService;
+    private IDistributionService distributionService;
 
     public CdmLightClassificationExport() {
         this.ioName = this.getClass().getSimpleName();
@@ -159,7 +166,7 @@ public class CdmLightClassificationExport
             if (state.getRootId() != null) {
                 List<TaxonNodeDto> childrenOfRoot = state.getNodeChildrenMap().get(state.getRootId());
 
-                Comparator<TaxonNodeDto> comp = state.getConfig().getComparator();
+                Comparator<TaxonNodeDto> comp = state.getConfig().getTaxonNodeComparator();
                 if (comp == null) {
                     comp = new TaxonNodeDtoByRankAndNameComparator();
                 }
@@ -216,7 +223,7 @@ public class CdmLightClassificationExport
         if (children == null) {
             return null;
         }
-        Comparator<TaxonNodeDto> comp = state.getConfig().getComparator();
+        Comparator<TaxonNodeDto> comp = state.getConfig().getTaxonNodeComparator();
         if (comp == null) {
             comp = new TaxonNodeDtoByRankAndNameComparator();
         }
@@ -424,6 +431,9 @@ public class CdmLightClassificationExport
     }
 
     private void handleDescriptions(CdmLightExportState state, CdmBase cdmBase) {
+        if (!state.getConfig().isDoFactualData()) {
+            return;
+        }
         String titleCache = null;
         try {
 
@@ -672,6 +682,33 @@ public class CdmLightClassificationExport
                 } else {
                     state.getProcessor().put(table, textData, csvLine);
                 }
+            }else if (element instanceof CategoricalData) {
+               //use formater
+               CategoricalData categoricalData = (CategoricalData)element;
+               String cache = CategoricalDataFormatter.NewInstance(null).format(categoricalData);
+               csvLine = new String[table.getSize()];
+                csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
+                if (cdmBase instanceof Taxon) {
+                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
+                } else if (cdmBase instanceof TaxonName) {
+                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, cdmBase);
+                }
+                csvLine[table.getIndex(CdmLightExportTable.FACT_TEXT)] = cache;
+                csvLine[table.getIndex(CdmLightExportTable.FACT_CATEGORY)] = categoricalData.getFeature().getLabel();
+                state.getProcessor().put(table, categoricalData, csvLine);
+            }else if (element instanceof QuantitativeData) {
+               QuantitativeData quantitativeData = (QuantitativeData) element;
+               String cache = QuantitativeDataFormatter.NewInstance(null).format(quantitativeData);
+               csvLine = new String[table.getSize()];
+                csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
+                if (cdmBase instanceof Taxon) {
+                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
+                } else if (cdmBase instanceof TaxonName) {
+                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, cdmBase);
+                }
+                csvLine[table.getIndex(CdmLightExportTable.FACT_TEXT)] = cache;
+                csvLine[table.getIndex(CdmLightExportTable.FACT_CATEGORY)] = quantitativeData.getFeature().getLabel();
+                state.getProcessor().put(table, quantitativeData, csvLine);
             }
         } catch (Exception e) {
             state.getResult().addException(e, "An unexpected error occurred when handling single simple fact "
@@ -801,13 +838,11 @@ public class CdmLightClassificationExport
                     }
                     state.getProcessor().put(table, source, csvLine);
                 }
-
             }
         } catch (Exception e) {
             state.getResult().addException(e, "An unexpected error occurred when handling single source "
                     + cdmBaseStr(element) + ": " + e.getMessage());
         }
-
     }
 
     private void handleDistributionFacts(CdmLightExportState state, Taxon taxon,
@@ -845,10 +880,11 @@ public class CdmLightClassificationExport
          if(state.getConfig().isCreateCondensedDistributionString()){
              List<Language> langs = new ArrayList<>();
              langs.add(Language.ENGLISH());
+             TermTree<NamedArea> areaTree = null; //TODO
 
-             CondensedDistribution conDis = geoService.getCondensedDistribution(
+             CondensedDistribution conDis = distributionService.getCondensedDistribution(
                      //TODO add CondensedDistributionConfiguration to export configuration
-                     distributions, true, null, state.getConfig().getCondensedDistributionConfiguration(), langs);
+                     distributions, areaTree, true, null, state.getConfig().getCondensedDistributionConfiguration(), langs);
              CdmLightExportTable tableCondensed =
                      CdmLightExportTable.SIMPLE_FACT;
              String[] csvLine = new String[tableCondensed.getSize()];
@@ -1342,7 +1378,7 @@ public class CdmLightClassificationExport
                     synonymsInGroup = acceptedTaxon.getSynonymsInGroup(group, comparator);
                 }
 
-                synonymsInGroup.stream().forEach(synonym -> typifiedNames.add(HibernateProxyHelper.deproxy(synonym.getName(), TaxonName.class)));
+                synonymsInGroup.stream().forEach(synonym -> typifiedNames.add(HibernateProxyHelper.deproxy(synonym.getName())));
 
             }else{
                 typifiedNames.addAll(group.getTypifiedNames());
@@ -1362,9 +1398,6 @@ public class CdmLightClassificationExport
         }
     }
 
-    /**
-     * @param specimenType
-     */
     private void handleSpecimenType_(CdmLightExportState state, SpecimenTypeDesignation specimenType) {
         if (specimenType.getTypeSpecimen() != null){
             DerivedUnit specimen =  specimenType.getTypeSpecimen();
@@ -1490,14 +1523,8 @@ public class CdmLightClassificationExport
             csvLine[table.getIndex(CdmLightExportTable.TYPIFIED_NAME_FK)] = getId(state, name);
         }
         state.getProcessor().put(table, specimenType, csvLine);
-
-
-
-
-
     }
 
-
     private String createNameWithItalics(List<TaggedText> taggedName) {
 
         String fullTitleWithHtml = "";
@@ -1525,11 +1552,11 @@ public class CdmLightClassificationExport
             if (!state.getNameStore().containsKey(name2.getId())) {
                 handleName(state, name2, null);
             }
-
+            csvLine = new String[table.getSize()];
             csvLine[table.getIndex(CdmLightExportTable.NAME_REL_TYPE)] = type.getLabel();
             csvLine[table.getIndex(CdmLightExportTable.NAME1_FK)] = getId(state, name);
             csvLine[table.getIndex(CdmLightExportTable.NAME2_FK)] = getId(state, name2);
-            state.getProcessor().put(table, name, csvLine);
+            state.getProcessor().put(table, rel.getUuid().toString(), csvLine);
         }
 
         rels = name.getRelationsToThisName();
@@ -1537,14 +1564,11 @@ public class CdmLightClassificationExport
         csvLine = new String[table.getSize()];
 
         for (NameRelationship rel : rels) {
-            NameRelationshipType type = rel.getType();
             TaxonName name2 = rel.getFromName();
-            name2 = HibernateProxyHelper.deproxy(name2, TaxonName.class);
+            name2 = HibernateProxyHelper.deproxy(name2);
             if (!state.getNameStore().containsKey(name2.getId())) {
                 handleName(state, name2, null);
             }
-
-
         }
     }
 
@@ -1586,9 +1610,9 @@ public class CdmLightClassificationExport
                     List<Identifier> identifiers = name.getIdentifiers();
 
                     //first check which kind of identifiers are available and then sort and create table entries
-                    Map<DefinedTerm, Set<Identifier>> identifierTypes = new HashMap<>();
+                    Map<IdentifierType, Set<Identifier>> identifierTypes = new HashMap<>();
                     for (Identifier identifier: identifiers){
-                        DefinedTerm type = identifier.getType();
+                        IdentifierType type = identifier.getType();
                         if (identifierTypes.containsKey(type)){
                             identifierTypes.get(type).add(identifier);
                         }else{
@@ -1598,7 +1622,7 @@ public class CdmLightClassificationExport
                         }
                     }
 
-                    for (DefinedTerm type:identifierTypes.keySet()){
+                    for (IdentifierType type:identifierTypes.keySet()){
                         Set<Identifier> identifiersByType = identifierTypes.get(type);
                         csvLine = new String[table.getSize()];
                         csvLine[table.getIndex(CdmLightExportTable.FK)] = getId(state, name);
@@ -1922,13 +1946,8 @@ public class CdmLightClassificationExport
                 Set<NameRelationship> related = name.getNameRelations();
                 List<NameRelationship> relatedList = new ArrayList<>(related);
 
-                Collections.sort(relatedList, new Comparator<NameRelationship>() {
-                    @Override
-                    public int compare(NameRelationship nr1, NameRelationship nr2) {
-                        return nr1.getType().compareTo(nr2.getType());
-                    }
-
-                });
+                Collections.sort(relatedList, (nr1, nr2)-> {
+                        return nr1.getType().compareTo(nr2.getType());});
 
                 List<NameRelationship> nonNames = new ArrayList<>();
                 List<NameRelationship> otherRelationships = new ArrayList<>();
@@ -1940,12 +1959,29 @@ public class CdmLightClassificationExport
                         if (rel.getType().equals(NameRelationshipType.LATER_HOMONYM())
                                 || rel.getType().equals(NameRelationshipType.TREATED_AS_LATER_HOMONYM())
                                 || (rel.getType().equals(NameRelationshipType.BLOCKING_NAME_FOR()))
-                                || (rel.getType().equals(NameRelationshipType.UNSPECIFIC_NON()))){
+                                || (rel.getType().equals(NameRelationshipType.UNSPECIFIC_NON()))
+                                || (rel.getType().equals(NameRelationshipType.AVOIDS_HOMONYM_OF()))
+                                ){
                             nonNames.add(rel);
                         }else if (!rel.getType().isBasionymRelation()){
                             otherRelationships.add(rel);
                         }
                     }
+                    if (state.getConfig().isShowInverseNameRelationsInHomotypicGroup()) {
+                       if (rel.getToName().equals(name)){
+                            // alle Homonyme und inverse blocking names
+//                               if (rel.getType().equals(NameRelationshipType.LATER_HOMONYM())
+//                                       || rel.getType().equals(NameRelationshipType.TREATED_AS_LATER_HOMONYM())
+//                                       || (rel.getType().equals(NameRelationshipType.BLOCKING_NAME_FOR()))
+//                                       || (rel.getType().equals(NameRelationshipType.UNSPECIFIC_NON()))
+//                                       || (rel.getType().equals(NameRelationshipType.AVOIDS_HOMONYM_OF()))
+//                                       ){
+//                                   nonNames.add(rel);
+//                               }else if (!rel.getType().isBasionymRelation()){
+                                   otherRelationships.add(rel);
+//                               }
+                           }
+                    }
                 }
 
                 String nonRelNames = "";
@@ -1959,22 +1995,25 @@ public class CdmLightClassificationExport
                     TaxonName relatedName = null;
                     if (relName.getFromName().equals(name)){
                         relatedName = relName.getToName();
-                        nonRelNames += label + relatedName.getTitleCache() + " ";
+                        if (state.getConfig().isAddHTML()){
+                               nonRelNames += label + createNameWithItalics(relatedName.getTaggedName())+ " ";
+                        }else{
+                               nonRelNames += label + relatedName.getTitleCache();
+                        }
                     }
 //                    else{
 //                        label = relName.getType().getInverseLabel() + " ";
 //                        relatedName = relName.getFromName();
 //                        nonRelNames += label + relatedName.getTitleCache() + " ";
 //                    }
-
-
                 }
-                relNames.trim();
+                nonRelNames.trim();
                 if (nonNames.size() > 0){
                     nonRelNames = StringUtils.strip(nonRelNames, null);
                     nonRelNames += "] ";
                 }
 
+                //other relationships
                 if (otherRelationships.size() > 0){
                     relNames += " [";
                 }
@@ -1990,11 +2029,15 @@ public class CdmLightClassificationExport
                             relNames += label + relatedName.getTitleCache();
                         }
                     }
-//                    else {
-//                        label = rel.getType().getInverseLabel() + " ";
-//                        relatedName = rel.getFromName();
-//                    }
-
+                    else {
+                        label = rel.getType().getInverseLabel() + " ";
+                        relatedName = rel.getFromName();
+                        if (state.getConfig().isAddHTML()){
+                            relNames += label + createNameWithItalics(relatedName.getTaggedName())+ " ";
+                        }else{
+                            relNames += label + relatedName.getTitleCache();
+                        }
+                    }
                 }
                 relNames.trim();
                 if (otherRelationships.size() > 0){
@@ -2002,6 +2045,7 @@ public class CdmLightClassificationExport
                     relNames += "] ";
                 }
 
+
                 String synonymSign = "";
                 if (index > 0){
                     if (name.isInvalid()){
@@ -2066,7 +2110,10 @@ public class CdmLightClassificationExport
                         }else{
                             doubtful = "";
                         }
-                        if (tb instanceof Synonym){
+                        if (tb instanceof Synonym ){
+                            if (!((Synonym)tb).getAcceptedTaxon().equals(acceptedTaxon)) {
+                                continue;
+                            }
                             if (StringUtils.isNotBlank(sec)){
                                 sec = " syn. sec. " + sec + " ";
                             }else {
@@ -2082,7 +2129,6 @@ public class CdmLightClassificationExport
                             }else {
                                 synonymSign = "\u003D ";
                             }
-
                         }
                     }
                     if (!isAccepted){