fix #6211 reduce initialization for synonymy

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java
index c77e59eccabd32ff505cf44e66d12be3f459a808..9f38ee3b2a34adea42328b3cb4e82583da71d291 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java
@@ -97,6 +97,8 @@ public class Taxon
     private static final long serialVersionUID = -584946869762749006L;
     private static final Logger logger = Logger.getLogger(Taxon.class);
 
+    private static final TaxonComparator defaultTaxonComparator = new TaxonComparator();
+
     @XmlElementWrapper(name = "Descriptions")
     @XmlElement(name = "Description")
     @OneToMany(mappedBy="taxon", fetch= FetchType.LAZY)
@@ -1160,11 +1162,13 @@ public class Taxon
      * @see                    eu.etaxonomy.cdm.model.name.HomotypicalGroup#getSynonymsInGroup(Reference)
      */
     @Transient
-    public List<Synonym> getHomotypicSynonymsByHomotypicGroup(){
+    public List<Synonym> getHomotypicSynonymsByHomotypicGroup(TaxonComparator comparator){
         if (this.getHomotypicGroup() == null){
             return null;
-        }else{
+        }else if (comparator == null){
             return this.getSynonymsInGroup(this.getHomotypicGroup());
+        }else{
+            return this.getSynonymsInGroup(this.getHomotypicGroup(), comparator);
         }
     }
 
@@ -1212,16 +1216,18 @@ public class Taxon
      */
     @Transient
     public List<HomotypicalGroup> getHomotypicSynonymyGroups(){
-        List<HomotypicalGroup> result = new ArrayList<HomotypicalGroup>();
-        result.add(this.getHomotypicGroup());
+        List<HomotypicalGroup> result = new ArrayList<>();
+        HomotypicalGroup myGroup = this.getHomotypicGroup();
+        if (myGroup != null){  //if taxon has no name HG might be null
+            result.add(myGroup);
+        }
         for (TaxonNameBase taxonNameBase :this.getSynonymNames()){
             if (taxonNameBase != null) {
                 if (!result.contains(taxonNameBase.getHomotypicalGroup())){
                     result.add(taxonNameBase.getHomotypicalGroup());
                 }
-            } // TODO: give error message to user
+            }
         }
-        // TODO: sort list according to date of first published name within each group
         return result;
     }
 
@@ -1275,9 +1281,10 @@ public class Taxon
     @Transient
     public List<HomotypicalGroup> getHeterotypicSynonymyGroups(){
         List<HomotypicalGroup> list = getHomotypicSynonymyGroups();
+        //remove homotypic group
         list.remove(this.getHomotypicGroup());
         //sort
-        Map<Synonym, HomotypicalGroup> map = new HashMap<Synonym, HomotypicalGroup>();
+        Map<Synonym, HomotypicalGroup> map = new HashMap<>();
         for (HomotypicalGroup homotypicalGroup: list){
             List<Synonym> synonymList = getSynonymsInGroup(homotypicalGroup);
             if (synonymList.size() > 0){
@@ -1285,13 +1292,14 @@ public class Taxon
                 map.put(synonymList.get(0), homotypicalGroup);
             }
         }
-        List<Synonym> keyList = new ArrayList<Synonym>();
+        List<Synonym> keyList = new ArrayList<>();
         keyList.addAll(map.keySet());
         //order by first synonym
-        Collections.sort(keyList, new TaxonComparator());
+        Collections.sort(keyList, defaultTaxonComparator);
 
-        List<HomotypicalGroup> result = new ArrayList<HomotypicalGroup>();
+        List<HomotypicalGroup> result = new ArrayList<>();
         for(Synonym synonym: keyList){
+            //"replace" synonyms by homotypic groups
             result.add(map.get(synonym));
         }
         //sort end
@@ -1327,16 +1335,25 @@ public class Taxon
      */
     @Transient
     public List<Synonym> getSynonymsInGroup(HomotypicalGroup homotypicGroup, TaxonComparator comparator){
-        List<Synonym> result = new ArrayList<Synonym>();
+        List<Synonym> result = new ArrayList<>();
+        if (homotypicGroup == null){
+            return result;  //always empty
+        }
 
-        for (TaxonNameBase<?, ?>name : homotypicGroup.getTypifiedNames()){
-            for (Synonym synonym : name.getSynonyms()){
-                Taxon accTaxon = synonym.getAcceptedTaxon();
-                if (accTaxon != null && accTaxon.equals(this) ) {
-                    result.add(synonym);
-                }
+        for (Synonym synonym : this.getSynonyms()){
+            if (homotypicGroup.equals(synonym.getHomotypicGroup())){
+                result.add(synonym);
             }
         }
+
+//        for (TaxonNameBase<?,?> name : homotypicGroup.getTypifiedNames()){
+//            for (Synonym synonym : name.getSynonyms()){
+//                Taxon accTaxon = synonym.getAcceptedTaxon();
+//                if (accTaxon != null && accTaxon.equals(this) ) {
+//                    result.add(synonym);
+//                }
+//            }
+//        }
         Collections.sort(result, comparator);
         return result;
     }

diff --git a/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonPortalController.java b/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonPortalController.java
index b328a10ba10d765cd4639d09db85fe4918e457d5..feddc1340cbfbcde9e76ea818160590f5f4feafc 100644 (file)
--- a/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonPortalController.java
+++ b/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonPortalController.java
@@ -120,9 +120,6 @@ public class TaxonPortalController extends TaxonController
     @Autowired
     private ITermService termService;
 
-    @Autowired
-    private IFeatureTreeService featureTreeService;
-
     private static final List<String> TAXON_INIT_STRATEGY = Arrays.asList(new String []{
             "$",
             "sources",
@@ -162,8 +159,8 @@ public class TaxonPortalController extends TaxonController
             "synonyms.name.status.type.representations",
             "synonyms.name.nomenclaturalReference.authorship",
             "synonyms.name.nomenclaturalReference.inReference",
-            "synonyms.name.homotypicalGroup.typifiedNames.$",
-            "synonyms.name.homotypicalGroup.typifiedNames.taxonBases.$",
+//            "synonyms.name.homotypicalGroup.typifiedNames.$",
+//            "synonyms.name.homotypicalGroup.typifiedNames.taxonBases.$",
             "synonyms.name.combinationAuthorship.$",
 
             "name.typeDesignations",
@@ -172,7 +169,7 @@ public class TaxonPortalController extends TaxonController
             "name.homotypicalGroup.typifiedNames.$",
             "name.homotypicalGroup.typifiedNames.nomenclaturalReference.authorship",
             "name.homotypicalGroup.typifiedNames.nomenclaturalReference.inReference",
-            "name.homotypicalGroup.typifiedNames.taxonBases.$"
+//            "name.homotypicalGroup.typifiedNames.taxonBases.$"
     });
 
 

diff --git a/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/json/processor/bean/TaxonBaseBeanProcessor.java b/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/json/processor/bean/TaxonBaseBeanProcessor.java
index e0d5af2e5ce97ef78d2034174065f114b0976967..512dbaa7a364e61396d5c9c8589253df12083fc1 100644 (file)
--- a/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/json/processor/bean/TaxonBaseBeanProcessor.java
+++ b/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/json/processor/bean/TaxonBaseBeanProcessor.java
@@ -46,7 +46,7 @@ public class TaxonBaseBeanProcessor extends AbstractCdmBeanProcessor<TaxonBase>
        @Override
        public List<String> getIgnorePropNames() {
                return Arrays.asList(new String[]{
-                               "acceptedTaxon"
+//                             "acceptedTaxon"  //#6211  to avoid infinite loops
                });
        }
 

diff --git a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonServiceImpl.java b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonServiceImpl.java
index a6a35e3e945f27db4528e73aa2819b951b053743..9dc00e414e64bc7da9465027a17c907a9ed8ca2e 100644 (file)
--- a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonServiceImpl.java
+++ b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonServiceImpl.java
@@ -104,6 +104,7 @@ import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
 import eu.etaxonomy.cdm.model.reference.Reference;
 import eu.etaxonomy.cdm.model.taxon.Classification;
+import eu.etaxonomy.cdm.model.taxon.HomotypicGroupTaxonComparator;
 import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
 import eu.etaxonomy.cdm.model.taxon.Synonym;
 import eu.etaxonomy.cdm.model.taxon.SynonymType;
@@ -597,16 +598,18 @@ public class TaxonServiceImpl extends IdentifiableServiceBase<TaxonBase,ITaxonDa
 
     @Override
     public List<List<Synonym>> getSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths){
-         List<List<Synonym>> result = new ArrayList<List<Synonym>>();
-        Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
+        List<List<Synonym>> result = new ArrayList<>();
+        taxon = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
+        HomotypicGroupTaxonComparator comparator = new HomotypicGroupTaxonComparator(taxon);
+
 
         //homotypic
-        result.add(t.getHomotypicSynonymsByHomotypicGroup());
+        result.add(taxon.getHomotypicSynonymsByHomotypicGroup(comparator));
 
         //heterotypic
-        List<HomotypicalGroup> homotypicalGroups = t.getHeterotypicSynonymyGroups();
+        List<HomotypicalGroup> homotypicalGroups = taxon.getHeterotypicSynonymyGroups();  //currently the list is sorted by the Taxon.defaultTaxonComparator
         for(HomotypicalGroup homotypicalGroup : homotypicalGroups){
-            result.add(t.getSynonymsInGroup(homotypicalGroup));
+            result.add(taxon.getSynonymsInGroup(homotypicalGroup, comparator));
         }
 
         return result;
@@ -616,14 +619,16 @@ public class TaxonServiceImpl extends IdentifiableServiceBase<TaxonBase,ITaxonDa
     @Override
     public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths){
         Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
-        return t.getHomotypicSynonymsByHomotypicGroup();
+        HomotypicGroupTaxonComparator comparator = new HomotypicGroupTaxonComparator(taxon);
+
+        return t.getHomotypicSynonymsByHomotypicGroup(comparator);
     }
 
     @Override
     public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths){
         Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
         List<HomotypicalGroup> homotypicalGroups = t.getHeterotypicSynonymyGroups();
-        List<List<Synonym>> heterotypicSynonymyGroups = new ArrayList<List<Synonym>>(homotypicalGroups.size());
+        List<List<Synonym>> heterotypicSynonymyGroups = new ArrayList<>(homotypicalGroups.size());
         for(HomotypicalGroup homotypicalGroup : homotypicalGroups){
             heterotypicSynonymyGroups.add(t.getSynonymsInGroup(homotypicalGroup));
         }

diff --git a/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceImplBusinessTest.java b/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceImplBusinessTest.java
index 74a24b64395fe5d0dc629d7a08f478c3523a6c56..ec8d46cd74a3913dcda523c78ced687b3ae2434f 100644 (file)
--- a/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceImplBusinessTest.java
+++ b/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonServiceImplBusinessTest.java
@@ -300,7 +300,7 @@ public class TaxonServiceImplBusinessTest extends CdmIntegrationTest {
                Assert.assertEquals("'homotypicSynonym' must have exactly 2 basionym relationships", 2, homotypicSynonym.getName().getNameRelations().size());
                Assert.assertEquals("'t1' must have exactly 1 basionym relationships", 1, t1.getName().getBasionyms().size());
                Assert.assertEquals("'t1' must have exactly 2 homotypic synonyms", 2, t1.getHomotypicSynonymsByHomotypicSynonymType().size());
-               Assert.assertEquals("'t1' must have exactly 2 names in homotypic group", 2, t1.getHomotypicSynonymsByHomotypicGroup().size());
+               Assert.assertEquals("'t1' must have exactly 2 names in homotypic group", 2, t1.getHomotypicSynonymsByHomotypicGroup(null).size());
                Assert.assertEquals("'t1' homotypic group must include 3 names (t1, s2, homotypicSynonym)", 3, t1.getHomotypicGroup().getTypifiedNames().size());
 
 
@@ -316,7 +316,7 @@ public class TaxonServiceImplBusinessTest extends CdmIntegrationTest {
                Assert.assertEquals("'homotypicSynonym' must have exactly 1 basionym relationships", 1, homotypicSynonym.getName().getNameRelations().size());
                Assert.assertEquals("'t1' must have exactly 1 basionym relationships", 1, t1.getName().getBasionyms().size());
                Assert.assertEquals("'t1' must have exactly 1 homotypic synonyms", 1, t1.getHomotypicSynonymsByHomotypicSynonymType().size());
-               Assert.assertEquals("'t1' must have exactly 1 names in homotypic group", 1, t1.getHomotypicSynonymsByHomotypicGroup().size());
+               Assert.assertEquals("'t1' must have exactly 1 names in homotypic group", 1, t1.getHomotypicSynonymsByHomotypicGroup(null).size());
                Assert.assertEquals("'t1' homotypic group must include 2 names (t1, homotypicSynonym)", 2, t1.getHomotypicGroup().getTypifiedNames().size());
 
                //do it