fixing probelms related to bean initialization

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonNode.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonNode.java
index 26734c237b592458083109557aee656b204e4190..2606a0fcceec5428a4b394cce248619c491b4d2f 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonNode.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonNode.java
@@ -231,12 +231,12 @@ public class TaxonNode extends AnnotatableEntity implements ITaxonTreeNode, ITre
 \r
         child.setParentTreeNode(this, index);\r
 \r
-               //TODO workaround (see sortIndex doc) => not really required anymore here, as it is done in child.setParentTreeNode already\r
-               for(int i = 0; i < childNodes.size(); i++){\r
-                       childNodes.get(i).sortIndex = i;\r
-               }\r
-               child.sortIndex = index;\r
-               \r
+        //TODO workaround (see sortIndex doc) => not really required anymore here, as it is done in child.setParentTreeNode already\r
+        for(int i = 0; i < childNodes.size(); i++){\r
+            childNodes.get(i).sortIndex = i;\r
+        }\r
+        child.sortIndex = index;\r
+\r
         //TODO workaround (see sortIndex doc)\r
         for(int i = 0; i < childNodes.size(); i++){\r
             childNodes.get(i).sortIndex = i;\r
@@ -519,23 +519,23 @@ public class TaxonNode extends AnnotatableEntity implements ITaxonTreeNode, ITre
         // add this node to the parent child nodes\r
         List<TaxonNode> parentChildren = parent.getChildNodes();\r
         if (parentChildren.contains(this)){\r
-               //avoid duplicates\r
-               if (parentChildren.indexOf(this) < index){\r
-                       index = index -1;\r
-               }\r
-               parentChildren.remove(this);\r
-               parentChildren.add(index, this);\r
+            //avoid duplicates\r
+            if (parentChildren.indexOf(this) < index){\r
+                index = index -1;\r
+            }\r
+            parentChildren.remove(this);\r
+            parentChildren.add(index, this);\r
         }else{\r
-               parentChildren.add(index, this);\r
+            parentChildren.add(index, this);\r
         }\r
 \r
         //TODO workaround (see sortIndex doc)\r
-        //TODO check if it is correct to use the parentChildren here \r
-               for(int i = 0; i < parentChildren.size(); i++){\r
-                       parentChildren.get(i).sortIndex = i;\r
-               }\r
+        //TODO check if it is correct to use the parentChildren here\r
+        for(int i = 0; i < parentChildren.size(); i++){\r
+            parentChildren.get(i).sortIndex = i;\r
+        }\r
 //             this.sortIndex = index;\r
-        \r
+\r
         // update the children count\r
         if(parent instanceof TaxonNode){\r
             TaxonNode parentTaxonNode = (TaxonNode) parent;\r

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonNodeByNameComparator.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonNodeByNameComparator.java
index 5ad4be0464013d58c30126c11eaa780645b55a39..67df308b6359111d2016b6c7249ec8da09d02e63 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonNodeByNameComparator.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonNodeByNameComparator.java
@@ -29,9 +29,9 @@ import eu.etaxonomy.cdm.model.name.TaxonNameBase;
 @Component\r
 public class TaxonNodeByNameComparator extends AbstractStringComparator<TaxonNode> implements Comparator<TaxonNode>, ITaxonNodeComparator<TaxonNode> {\r
 \r
-       private static final String HYBRID_SIGN = "\u00D7";\r
+    private static final String HYBRID_SIGN = "\u00D7";\r
 \r
-       private static final Logger logger = Logger.getLogger(TaxonNodeByNameComparator.class);\r
+    private static final Logger logger = Logger.getLogger(TaxonNodeByNameComparator.class);\r
 \r
     private boolean ignoreHybridSign = true;\r
     private boolean sortInfraGenericFirst = true;\r
@@ -39,13 +39,14 @@ public class TaxonNodeByNameComparator extends AbstractStringComparator<TaxonNod
     /* (non-Javadoc)\r
      * @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)\r
      */\r
+    @Override\r
     public int compare(TaxonNode o1, TaxonNode o2) {\r
 \r
         String titleCache1 = createSortableTitleCache(o1);\r
         String titleCache2 = createSortableTitleCache(o2);\r
 \r
         if(isIgnoreHybridSign()) {\r
-               logger.trace("ignoring Hybrid Signs: " + HYBRID_SIGN);\r
+            logger.trace("ignoring Hybrid Signs: " + HYBRID_SIGN);\r
             titleCache1 = titleCache1.replace(HYBRID_SIGN, "");\r
             titleCache2 = titleCache2.replace(HYBRID_SIGN, "");\r
         }\r
@@ -76,49 +77,51 @@ public class TaxonNodeByNameComparator extends AbstractStringComparator<TaxonNod
     }\r
 \r
 \r
-       private String createSortableTitleCache(TaxonNode taxonNode) {\r
+    private String createSortableTitleCache(TaxonNode taxonNode) {\r
 \r
-               String titleCache = null;\r
-               if(taxonNode.getTaxon() != null && taxonNode.getTaxon().getName() != null ){\r
-                       TaxonNameBase<?,?> name = HibernateProxyHelper.deproxy(taxonNode.getTaxon().getName(), TaxonNameBase.class);\r
-               \r
-                       if (name instanceof NonViralName){\r
-                               if (logger.isTraceEnabled()){logger.trace(name + " isNonViralName");}\r
-               NonViralName<?> nonViralName = (NonViralName<?>)name;\r
+        String titleCache = null;\r
+        if(taxonNode.getTaxon() != null && taxonNode.getTaxon().getName() != null ){\r
+            TaxonNameBase<?,?> name = HibernateProxyHelper.deproxy(taxonNode.getTaxon().getName(), TaxonNameBase.class);\r
+\r
+            if (name instanceof NonViralName){\r
+                if (logger.isTraceEnabled()){logger.trace(name + " isNonViralName");}\r
+                NonViralName<?> nonViralName = (NonViralName<?>)name;\r
                 if (name.isInfraSpecific()){\r
-                       if (logger.isTraceEnabled()){logger.trace(name + " isInfraSpecific");}\r
+                    if (logger.isTraceEnabled()){logger.trace(name + " isInfraSpecific");}\r
                     if (nonViralName.getSpecificEpithet().equals(nonViralName.getInfraSpecificEpithet())){\r
                         titleCache = nonViralName.getNameCache() + " "+nonViralName.getAuthorshipCache();\r
                     }\r
                 }\r
                 if (name.isInfraGeneric()){\r
-                       if (logger.isTraceEnabled()){logger.trace(name + " isInfraGeneric");}\r
-                       titleCache = nonViralName.getGenusOrUninomial() + " " + nonViralName.getInfraGenericEpithet();\r
+                    if (logger.isTraceEnabled()){logger.trace(name + " isInfraGeneric");}\r
+                    titleCache = nonViralName.getGenusOrUninomial() + " " + nonViralName.getInfraGenericEpithet();\r
                 }\r
                 if (nonViralName.isSpeciesAggregate()){\r
-                       if (logger.isTraceEnabled()){logger.trace(name + " isSpeciesAggregate");}\r
-                       titleCache = nonViralName.getGenusOrUninomial() + " " + nonViralName.getSpecificEpithet();\r
+                    if (logger.isTraceEnabled()){logger.trace(name + " isSpeciesAggregate");}\r
+                    titleCache = nonViralName.getGenusOrUninomial() + " " + nonViralName.getSpecificEpithet();\r
                 }\r
 \r
             }\r
             if (titleCache == null){\r
-               if (logger.isTraceEnabled()){logger.trace("titleCache still null, using name.getTitleCache()");}\r
+                if (logger.isTraceEnabled()){logger.trace("titleCache still null, using name.getTitleCache()");}\r
                 titleCache = name.getTitleCache();\r
             }\r
         }\r
-               if (titleCache == null){\r
-                       if (logger.isTraceEnabled()){logger.trace("titleCache still null, using taxonNode id");}\r
+        if (titleCache == null){\r
+            if (logger.isTraceEnabled()){logger.trace("titleCache still null, using taxonNode id");}\r
             titleCache = String.valueOf(taxonNode.getId());\r
         }\r
         if (logger.isTraceEnabled()){logger.trace("SortableTitleCache: " + titleCache);}\r
-               return titleCache;\r
-       }\r
+        return titleCache;\r
+    }\r
 \r
 \r
+    @Override\r
     public boolean isIgnoreHybridSign() {\r
         return ignoreHybridSign;\r
     }\r
 \r
+    @Override\r
     public void setIgnoreHybridSign(boolean ignore) {\r
         this.ignoreHybridSign = ignore;\r
     }\r

diff --git a/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/ClassificationPortalListController.java b/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/ClassificationPortalListController.java
index 412834eba08d4fe4b2ab6fefc45d3dca5cff48ba..9aa7afe544b3f73cdc45ce31eaf55272b94806d9 100644 (file)
--- a/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/ClassificationPortalListController.java
+++ b/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/ClassificationPortalListController.java
@@ -51,7 +51,7 @@ public class ClassificationPortalListController extends IdentifiableListControll
 \r
     private static final List<String> NODE_INIT_STRATEGY = Arrays.asList(new String[]{\r
             "taxon.sec",\r
-            "taxon.name"\r
+            "taxon.name.rank"\r
             });\r
 \r
 \r

diff --git a/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/DescriptionListPortalController.java b/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/DescriptionListPortalController.java
index 596a154ad04040c8b677d3ce14f0ecac03e50de6..27b8e40e8095ad79499594bda8adef60e6b26f16 100644 (file)
--- a/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/DescriptionListPortalController.java
+++ b/cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/DescriptionListPortalController.java
@@ -64,6 +64,8 @@ public class DescriptionListPortalController extends IdentifiableListController<
     protected static final List<String> DESCRIPTION_INIT_STRATEGY = Arrays.asList(new String []{\r
             "$",\r
             "elements.$",\r
+            "elements.annotations",\r
+            "elements.markers",\r
             "elements.states.$",\r
             "elements.sources.citation.authorTeam",\r
             "elements.sources.nameUsedInSource.originalNameString",\r
@@ -77,6 +79,8 @@ public class DescriptionListPortalController extends IdentifiableListController<
 \r
     protected static final List<String> DESCRIPTION_ELEMENT_INIT_STRATEGY = Arrays.asList(new String []{\r
             "$",\r
+            "annotations",\r
+            "markers",\r
             "states.$",\r
             "sources.citation.authorTeam",\r
             "sources.nameUsedInSource.originalNameString",\r
@@ -212,7 +216,7 @@ public class DescriptionListPortalController extends IdentifiableListController<
            }\r
        }\r
        //TODO it seems as if the InitializationStrategy is not appropriate here !!!\r
-       //   see #3728 (DescriptionListPortalController.getDescriptionElementsForTaxon() seems to be using inapproptiate init strategy)\r
+       //   see #3728 (DescriptionListPortalController.getDescriptionElementsForTaxon() seems to be using in-appropriate init strategy)\r
        if (logger.isDebugEnabled()){logger.debug("get pager ...");}\r
        Pager<T> pager = service.pageDescriptionElementsForTaxon(\r
                taxon,\r

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 5b29421f45a2af8e823dd4fc89332b63cf6b1b48..5a80f88a9ee81b3e22f1fad1c8f12d74a64c3dc9 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
@@ -138,18 +138,18 @@ public class TaxonPortalController extends BaseController<TaxonBase, ITaxonServi
     private IFeatureTreeService featureTreeService;\r
 \r
     private static final List<String> TAXON_INIT_STRATEGY = Arrays.asList(new String []{\r
-            "*",\r
+            "$",\r
+            "sources",\r
             // taxon relations\r
-            "relationsToThisName.fromTaxon.name",\r
+//            "relationsToThisName.fromTaxon.name",\r
             // the name\r
             "name.$",\r
+            "name.nomenclaturalReference.authorTeam",\r
+            "name.nomenclaturalReference.inReference",\r
             "name.rank.representations",\r
             "name.status.type.representations",\r
 \r
-            // taxon descriptions\r
-//            "descriptions.elements.area.$",\r
-//            "descriptions.elements.multilanguageText",\r
-//            "descriptions.elements.media",\r
+            "descriptions" // TODO remove\r
 \r
             });\r
 \r
@@ -165,7 +165,9 @@ public class TaxonPortalController extends BaseController<TaxonBase, ITaxonServi
             "name.$",\r
             "name.rank.representations",\r
             "name.status.type.representations",\r
-            "name.nomenclaturalReference.authorTeam"\r
+            "name.nomenclaturalReference.authorTeam",\r
+            "name.nomenclaturalReference.inReference",\r
+            "taxonNodes.classification"\r
             });\r
 \r
     private static final List<String> SYNONYMY_INIT_STRATEGY = Arrays.asList(new String []{\r
@@ -173,6 +175,7 @@ public class TaxonPortalController extends BaseController<TaxonBase, ITaxonServi
             "synonymRelations.$",\r
             "synonymRelations.synonym.$",\r
             "synonymRelations.synonym.name.status.type.representation",\r
+            "synonymRelations.synonym.name.nomenclaturalReference.authorTeam",\r
             "synonymRelations.synonym.name.nomenclaturalReference.inReference",\r
             "synonymRelations.synonym.name.homotypicalGroup.typifiedNames.$",\r
             "synonymRelations.synonym.name.homotypicalGroup.typifiedNames.taxonBases.$",\r
@@ -183,7 +186,7 @@ public class TaxonPortalController extends BaseController<TaxonBase, ITaxonServi
             "name.homotypicalGroup.$",\r
             "name.homotypicalGroup.typifiedNames.$",\r
             "name.homotypicalGroup.typifiedNames.nomenclaturalReference.authorTeam",\r
-\r
+            "name.homotypicalGroup.typifiedNames.nomenclaturalReference.inReference",\r
             "name.homotypicalGroup.typifiedNames.taxonBases.$"\r
     });\r
 \r
@@ -192,6 +195,7 @@ public class TaxonPortalController extends BaseController<TaxonBase, ITaxonServi
             "synonymRelations.$",\r
             "synonymRelations.synonym.$",\r
             "synonymRelations.synonym.name.status.type.representation",\r
+            "synonymRelations.synonym.name.nomenclaturalReference.authorTeam",\r
             "synonymRelations.synonym.name.nomenclaturalReference.inReference",\r
             "synonymRelations.synonym.name.homotypicalGroup.typifiedNames.$",\r
             "synonymRelations.synonym.name.homotypicalGroup.typifiedNames.taxonBases.$",\r
@@ -200,6 +204,7 @@ public class TaxonPortalController extends BaseController<TaxonBase, ITaxonServi
             "name.homotypicalGroup.$",\r
             "name.homotypicalGroup.typifiedNames.$",\r
             "name.homotypicalGroup.typifiedNames.nomenclaturalReference.authorTeam",\r
+            "name.homotypicalGroup.typifiedNames.nomenclaturalReference.inReference",\r
 \r
             "name.homotypicalGroup.typifiedNames.taxonBases.$",\r
 \r
@@ -215,7 +220,8 @@ public class TaxonPortalController extends BaseController<TaxonBase, ITaxonServi
             "name.$",\r
             "name.rank.representations",\r
             "name.status.type.representations",\r
-            "name.nomenclaturalReference",\r
+            "name.nomenclaturalReference.authorTeam",\r
+            "name.nomenclaturalReference.inReference",\r
 \r
             "taxonNodes.$",\r
             "taxonNodes.classification.$",\r
@@ -237,6 +243,9 @@ public class TaxonPortalController extends BaseController<TaxonBase, ITaxonServi
             "type.inverseRepresentations",\r
             "fromName",\r
             "toName.$",\r
+            "toName.nomenclaturalReference.authorTeam",\r
+            "toName.nomenclaturalReference.inReference",\r
+\r
     });\r
 \r
 \r