cleanup

diff --git a/cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/SetMap.java b/cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/SetMap.java
index aa1635a2e0bbb043cc9896f43811bac42e424332..b3626b150ea180245853f909c4a00174db0f931b 100644 (file)
--- a/cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/SetMap.java
+++ b/cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/SetMap.java
@@ -61,7 +61,7 @@ public class SetMap<K,V> implements Map<K, Set<V>>{
 
     @Override
     public boolean containsValue(Object value) {
-        return map.containsKey(value);
+        return map.containsValue(value); //TODO shouldn't we check for a single value in the set?
     }
 
     /**

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/markup/MarkupImportBase.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/markup/MarkupImportBase.java
index 152da4765615a774e50f667ddf4810873ad640ce..de7933ba9949a088facf1a79e0d357fd822fce53 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/markup/MarkupImportBase.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/markup/MarkupImportBase.java
@@ -2450,7 +2450,7 @@ public abstract class MarkupImportBase  {
                                                        if (isNotBlank(innerArea)){
                                                                NamedArea singleArea = makeArea(state, innerArea.trim(), level);
                                                                areas.add(singleArea);
-                                                               NamedArea partOf = singleArea.getPartOf();
+//                                                             NamedArea partOf = singleArea.getPartOf();
 //                                                             if (partOf == null){
 //                                                                     singleArea.setPartOf(higherArea);
 //                                                             }

diff --git a/cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/jaxb/TermTest.java b/cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/jaxb/TermTest.java
index aeb3a224c6b104378ac566145bb672f1e979a8ef..7171e9aef7d5630183a791c7878702d82e62841e 100644 (file)
--- a/cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/jaxb/TermTest.java
+++ b/cdmlib-io/src/test/java/eu/etaxonomy/cdm/io/jaxb/TermTest.java
@@ -1,56 +1,56 @@
-/**\r
-* Copyright (C) 2009 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.cdm.io.jaxb;\r
-\r
-import static org.junit.Assert.assertEquals;\r
-import static org.junit.Assert.assertFalse;\r
-import static org.junit.Assert.assertNotNull;\r
-import static org.junit.Assert.assertTrue;\r
-\r
-import java.io.InputStreamReader;\r
-import eu.etaxonomy.cdm.common.URI;\r
-\r
-import org.junit.Test;\r
-\r
-import eu.etaxonomy.cdm.model.description.Feature;\r
-import eu.etaxonomy.cdm.model.location.NamedArea;\r
-\r
-public class TermTest {\r
-\r
-           private String resource = "/eu/etaxonomy/cdm/io/jaxb/TermTest.xml";\r
-\r
-           @Test\r
-           public void testUnmarshalTerm() throws Exception {\r
-               CdmDocumentBuilder cdmDocumentBuilder = new CdmDocumentBuilder();\r
-               URI uri = new URI(URIEncoder.encode(this.getClass().getResource(resource).toString()));\r
-               DataSet dataSet = cdmDocumentBuilder.unmarshal(DataSet.class, new InputStreamReader(this.getClass().getResourceAsStream(resource)),uri.toString());\r
-\r
-                       NamedArea africa = (NamedArea)dataSet.getTerms().get(2);\r
-                       assertNotNull("DefinedTermBase must not be null", africa);\r
-                       assertNotNull("DefinedTermBase.includes must not be null", africa.getIncludes());\r
-                       assertFalse("DefinedTermBase.includes must contain NamedArea instances", africa.getIncludes().isEmpty());\r
-                       assertEquals("DefinedTermBase.includes must contain eight NamedArea instances", 8, africa.getIncludes().size());\r
-                       NamedArea northAfrica = (NamedArea)dataSet.getTerms().get(4);\r
-                       assertNotNull("DefinedTermBase must not be null", northAfrica);\r
-                       assertTrue("Africa must include North Africa", africa.getIncludes().contains(northAfrica));\r
-                       assertNotNull("DefinedTermBase.partOf must not be null", northAfrica.getPartOf());\r
-                       assertEquals("North Africa must be part of Africa",africa, northAfrica.getPartOf());\r
-\r
-                       Feature discussion = (Feature)dataSet.getTerms().get(13);\r
-                       assertNotNull("DefinedTermBase must not be null", discussion);\r
-                       assertNotNull("DefinedTermBase.generalizationOf must not be null", discussion.getGeneralizationOf());\r
-                       assertFalse("DefinedTermBase.generalizationOf must contain Feature instances", discussion.getGeneralizationOf().isEmpty());\r
-                       assertEquals("DefinedTermBase.generalizationOf must contain two Feature instances", 2, discussion.getGeneralizationOf().size());\r
-                       Feature taxonomicDiscussion = (Feature)dataSet.getTerms().get(14);\r
-                       assertNotNull("DefinedTermBase must not be null",taxonomicDiscussion);\r
-                       assertTrue("Discussion must be the generalization of Taxonomic Discussion", discussion.getGeneralizationOf().contains(taxonomicDiscussion));\r
-                       assertNotNull("DefinedTermBase.kindOf must not be null", taxonomicDiscussion.getKindOf());\r
-                       assertEquals("Taxonomic Discussion must be a kind of Discussion", discussion, taxonomicDiscussion.getKindOf());\r
-           }\r
-}\r
+/**
+* Copyright (C) 2009 EDIT
+* European Distributed Institute of Taxonomy
+* http://www.e-taxonomy.eu
+*
+* The contents of this file are subject to the Mozilla Public License Version 1.1
+* See LICENSE.TXT at the top of this package for the full license terms.
+*/
+package eu.etaxonomy.cdm.io.jaxb;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.InputStreamReader;
+
+import org.junit.Test;
+
+import eu.etaxonomy.cdm.common.URI;
+import eu.etaxonomy.cdm.model.description.Feature;
+import eu.etaxonomy.cdm.model.location.NamedArea;
+
+public class TermTest {
+
+           private String resource = "/eu/etaxonomy/cdm/io/jaxb/TermTest.xml";
+
+           @Test
+           public void testUnmarshalTerm() throws Exception {
+               CdmDocumentBuilder cdmDocumentBuilder = new CdmDocumentBuilder();
+               URI uri = new URI(URIEncoder.encode(this.getClass().getResource(resource).toString()));
+               DataSet dataSet = cdmDocumentBuilder.unmarshal(DataSet.class, new InputStreamReader(this.getClass().getResourceAsStream(resource)),uri.toString());
+
+                       NamedArea africa = (NamedArea)dataSet.getTerms().get(2);
+                       assertNotNull("DefinedTermBase must not be null", africa);
+                       assertNotNull("DefinedTermBase.includes must not be null", africa.getIncludes());
+                       assertFalse("DefinedTermBase.includes must contain NamedArea instances", africa.getIncludes().isEmpty());
+                       assertEquals("DefinedTermBase.includes must contain eight NamedArea instances", 8, africa.getIncludes().size());
+                       NamedArea northAfrica = (NamedArea)dataSet.getTerms().get(4);
+                       assertNotNull("DefinedTermBase must not be null", northAfrica);
+                       assertTrue("Africa must include North Africa", africa.getIncludes().contains(northAfrica));
+                       assertNotNull("DefinedTermBase.partOf must not be null", northAfrica.getPartOf());
+                       assertEquals("North Africa must be part of Africa",africa, northAfrica.getPartOf());
+
+                       Feature discussion = (Feature)dataSet.getTerms().get(13);
+                       assertNotNull("DefinedTermBase must not be null", discussion);
+                       assertNotNull("DefinedTermBase.generalizationOf must not be null", discussion.getGeneralizationOf());
+                       assertFalse("DefinedTermBase.generalizationOf must contain Feature instances", discussion.getGeneralizationOf().isEmpty());
+                       assertEquals("DefinedTermBase.generalizationOf must contain two Feature instances", 2, discussion.getGeneralizationOf().size());
+                       Feature taxonomicDiscussion = (Feature)dataSet.getTerms().get(14);
+                       assertNotNull("DefinedTermBase must not be null",taxonomicDiscussion);
+                       assertTrue("Discussion must be the generalization of Taxonomic Discussion", discussion.getGeneralizationOf().contains(taxonomicDiscussion));
+                       assertNotNull("DefinedTermBase.kindOf must not be null", taxonomicDiscussion.getKindOf());
+                       assertEquals("Taxonomic Discussion must be a kind of Discussion", discussion, taxonomicDiscussion.getKindOf());
+           }
+}
\ No newline at end of file

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/format/description/distribution/CondensedDistributionComposer.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/format/description/distribution/CondensedDistributionComposer.java
index 270ceaa794a3f1fcc39a4bb36bc9baf27a9a9153..05f45dbe592a3a6fc20702c7691ca5eecd9fd401 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/format/description/distribution/CondensedDistributionComposer.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/format/description/distribution/CondensedDistributionComposer.java
@@ -372,27 +372,7 @@ public class CondensedDistributionComposer {
         return config.statusForBoldAreas.contains(status.getUuid());
     }
 
-    /**
-     * Searches for the parent area of the area given as parameter in
-     * the collection of areas.
-     *
-     * @parent area
-     *      The area which parent area is to be searched
-     * @param collection
-     *      The areas to search in.
-     *
-     * @return
-     *      Either the parent if it has been found or null.
-     */
-    protected NamedArea findParentIn(NamedArea area, Collection<NamedArea> areas) {
-        NamedArea parent = area.getPartOf();
-        if(parent != null && areas.contains(parent)){
-            return parent;
-        }
-        return null;
-    }
-
-    protected class AreaNode {
+    private class AreaNode {
 
         protected final NamedArea area;
         protected AreaNode parent = null;

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/DefinedTermBaseClassBridge.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/DefinedTermBaseClassBridge.java
index b710f0b2d11935d72ef4484e4b0468da9a55b44e..16b5633a40fd6a62a83d0ff954e21128d05a9496 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/DefinedTermBaseClassBridge.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/search/DefinedTermBaseClassBridge.java
@@ -23,7 +23,6 @@ import eu.etaxonomy.cdm.model.term.Representation;
 /**
  * @author Andreas Kohlbecker
  * @since Jun 4, 2012
- *
  */
 public class DefinedTermBaseClassBridge extends AbstractClassBridge implements ParameterizedBridge {
 
@@ -31,7 +30,6 @@ public class DefinedTermBaseClassBridge extends AbstractClassBridge implements P
 
     private boolean includeParentTerms = false;
 
-
     @Override
     public void set(String name, Object value, Document document, LuceneOptions luceneOptions) {
 

diff --git a/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/location/NamedAreaTest.java b/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/location/NamedAreaTest.java
index a4a0840bf49fa45c7dd20527028b08391544f09a..6bc55f0d854fd0a328e96ee8ce68f2463e64e4a8 100644 (file)
--- a/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/location/NamedAreaTest.java
+++ b/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/location/NamedAreaTest.java
@@ -63,6 +63,7 @@ public class NamedAreaTest extends EntityTestBase {
 
        @Test
        public void getHiearchieListTest(){
+
                //Create example data
                List<NamedArea> list = new ArrayList<>();
                NamedArea germanyL4 = getAreaByTdwgAbbreviation("GER-OO");

diff --git a/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/location/TdwgAreaTest.java b/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/location/TdwgAreaTest.java
index abee08f18a8ddee6bfe08ebc026a5fd7b968e172..3d02b899b4a69fc40cbc87f0225aefa7d8d0631f 100644 (file)
--- a/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/location/TdwgAreaTest.java
+++ b/cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/location/TdwgAreaTest.java
@@ -88,8 +88,8 @@ public class TdwgAreaTest extends EntityTestBase {
                assert britain != null : "NamedArea must exist";
                assert northernEurope != null : "NamedArea must exist";
 
-               Assert.assertTrue("Northern Europe should include Britain",northernEurope.getIncludes().contains(britain));
-               assertEquals("Britain should be part of Northern Europe",britain.getPartOf(),northernEurope);
+               Assert.assertTrue("Northern Europe should include Britain", northernEurope.getIncludes().contains(britain));
+               assertEquals("Britain should be part of Northern Europe", britain.getPartOf(),northernEurope);
        }
 
        @Test
@@ -243,15 +243,6 @@ public class TdwgAreaTest extends EntityTestBase {
                return result;
        }
 
-       //PRE: in parameter tdwg can not be smaller than the current tdwglevel of the second parameter
-       public static NamedArea getAreaLabelForTDWGLevel(Integer tdwgLevel, NamedArea area){
-               NamedArea aux = area;
-               while (aux.getLevel().getLabel().toString().compareTo("TDWG Level " + tdwgLevel.toString()) != 0) {
-                       aux = aux.getPartOf();
-               }
-               return aux;
-       }
-
        private NamedArea getAreaByTdwgAbbreviation(String tdwgAbbrev){
                return NamedArea.getAreaByTdwgAbbreviation(tdwgAbbrev);
        }

diff --git a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dto/TermDto.java b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dto/TermDto.java
index 50a92b20653a4f302e04111ee0f9a2d4255fc966..9fd8866a43dfad4d7c446a59f156d9ea7494ebdb 100644 (file)
--- a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dto/TermDto.java
+++ b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dto/TermDto.java
@@ -80,7 +80,7 @@ public class TermDto extends AbstractTermDto{
         DefinedTermBase<?> kindOf = term.getKindOf();
         TermVocabulary<?> vocabulary = term.getVocabulary();
         if (representations == null){
-            term = HibernateProxyHelper.deproxy(term, DefinedTermBase.class);
+            term = HibernateProxyHelper.deproxy(term);
             representations = term.getRepresentations();
         }
 

diff --git a/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/geo/DistributionServiceImplTest.java b/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/geo/DistributionServiceImplTest.java
index e8656eeb65206968aa069a7358c4b8c9fc6b496b..0babc2c70b4e7b8597ad130e4e45f6a08c0cf7e1 100644 (file)
--- a/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/geo/DistributionServiceImplTest.java
+++ b/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/geo/DistributionServiceImplTest.java
@@ -263,6 +263,7 @@ public class DistributionServiceImplTest extends CdmTransactionalIntegrationTest
         distributionService.mapShapeFileToNamedAreas(new InputStreamReader(is), idSearchFields, wmsLayerName, uuidCyprusDivisionsVocabulary, null);
 
         divisions.clear();
+        @SuppressWarnings("unchecked")
         Set<DefinedTermBase> terms = vocabService.load(uuidCyprusDivisionsVocabulary).getTerms();
         for(DefinedTermBase<?> dtb : terms){
             divisions.put(dtb.getIdInVocabulary(), (NamedArea) dtb);