- fix cdmlib version number in .classpath (why does maven not generate this anymore?)

 - added "molecular" package to exported packages
 - organize imports for new molecular services

diff --git a/eu.etaxonomy.taxeditor.cdmlib/.classpath b/eu.etaxonomy.taxeditor.cdmlib/.classpath
index 029e764d05650ba49bd513dd1f0635617f07815a..a429deef46005f7d150622513cc03335900d2b65 100644 (file)
--- a/eu.etaxonomy.taxeditor.cdmlib/.classpath
+++ b/eu.etaxonomy.taxeditor.cdmlib/.classpath
@@ -28,22 +28,22 @@
        <classpathentry exported="true" kind="lib" path="lib/batik-util-1.7.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/batik-xml-1.7.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/c3p0-0.9.2.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-commons-3.3.1-SNAPSHOT-sources.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-commons-3.3.1-SNAPSHOT.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-3.3.1-SNAPSHOT-sources.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-3.3.1-SNAPSHOT.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-io-3.3.1-SNAPSHOT-sources.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-io-3.3.1-SNAPSHOT.jar" sourcepath="lib/cdmlib-io-3.3.1-SNAPSHOT-sources.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.3.1-SNAPSHOT-sources.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.3.1-SNAPSHOT.jar" sourcepath="lib/cdmlib-model-3.3.1-SNAPSHOT-sources.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-3.3.1-SNAPSHOT-sources.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-3.3.1-SNAPSHOT.jar" sourcepath="lib/cdmlib-persistence-3.3.1-SNAPSHOT-sources.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-print-3.3.1-SNAPSHOT-sources.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-print-3.3.1-SNAPSHOT.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-3.3.1-SNAPSHOT-sources.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-3.3.1-SNAPSHOT.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-services-3.3.1-SNAPSHOT-sources.jar"/>
-       <classpathentry exported="true" kind="lib" path="lib/cdmlib-services-3.3.1-SNAPSHOT.jar" sourcepath="lib/cdmlib-services-3.3.1-SNAPSHOT-sources.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-commons-3.3.2-SNAPSHOT-sources.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-commons-3.3.2-SNAPSHOT.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-3.3.2-SNAPSHOT-sources.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-3.3.2-SNAPSHOT.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-io-3.3.2-SNAPSHOT-sources.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-io-3.3.2-SNAPSHOT.jar" sourcepath="lib/cdmlib-io-3.3.2-SNAPSHOT-sources.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.3.2-SNAPSHOT-sources.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.3.2-SNAPSHOT.jar" sourcepath="lib/cdmlib-model-3.3.2-SNAPSHOT-sources.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-3.3.2-SNAPSHOT-sources.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-3.3.2-SNAPSHOT.jar" sourcepath="lib/cdmlib-persistence-3.3.2-SNAPSHOT-sources.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-print-3.3.2-SNAPSHOT-sources.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-print-3.3.2-SNAPSHOT.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-3.3.2-SNAPSHOT-sources.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-3.3.2-SNAPSHOT.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-services-3.3.2-SNAPSHOT-sources.jar"/>
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-services-3.3.2-SNAPSHOT.jar" sourcepath="lib/cdmlib-services-3.3.2-SNAPSHOT-sources.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/cglib-nodep-2.2.2.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/com.springsource.org.aopalliance-1.0.0.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/com.springsource.org.apache.commons.logging-1.1.1.jar"/>

diff --git a/eu.etaxonomy.taxeditor.cdmlib/META-INF/MANIFEST.MF b/eu.etaxonomy.taxeditor.cdmlib/META-INF/MANIFEST.MF
index 8aa9167687708632e64a5e5f739de031f4c591ad..a2805f84696a79774b81f784d606c133e2a13d79 100644 (file)
--- a/eu.etaxonomy.taxeditor.cdmlib/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.cdmlib/META-INF/MANIFEST.MF
@@ -17,6 +17,7 @@ Export-Package: com.google.api,
  eu.etaxonomy.cdm.api.service.exception,
  eu.etaxonomy.cdm.api.service.lsid,
  eu.etaxonomy.cdm.api.service.lsid.impl,
+ eu.etaxonomy.cdm.api.service.molecular,
  eu.etaxonomy.cdm.api.service.pager,
  eu.etaxonomy.cdm.api.service.pager.impl,
  eu.etaxonomy.cdm.api.service.search,

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientCdmRepository.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientCdmRepository.java
index 9b8f6f1bc6f6881536de494d98e7072475c12b1a..6fa951d9a4064a9065f62e7c3d185ec7aaa99f5e 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientCdmRepository.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientCdmRepository.java
@@ -18,7 +18,6 @@ import org.springframework.transaction.TransactionStatus;
 import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
 import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
 import eu.etaxonomy.cdm.api.service.IAgentService;
-import eu.etaxonomy.cdm.api.service.IAmplificationService;
 import eu.etaxonomy.cdm.api.service.IClassificationService;
 import eu.etaxonomy.cdm.api.service.ICollectionService;
 import eu.etaxonomy.cdm.api.service.ICommonService;
@@ -35,9 +34,7 @@ import eu.etaxonomy.cdm.api.service.INameService;
 import eu.etaxonomy.cdm.api.service.IOccurrenceService;
 import eu.etaxonomy.cdm.api.service.IPolytomousKeyNodeService;
 import eu.etaxonomy.cdm.api.service.IPolytomousKeyService;
-import eu.etaxonomy.cdm.api.service.IPrimerService;
 import eu.etaxonomy.cdm.api.service.IReferenceService;
-import eu.etaxonomy.cdm.api.service.ISequenceService;
 import eu.etaxonomy.cdm.api.service.IService;
 import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
 import eu.etaxonomy.cdm.api.service.ITaxonService;
@@ -45,6 +42,9 @@ import eu.etaxonomy.cdm.api.service.ITermService;
 import eu.etaxonomy.cdm.api.service.IUserService;
 import eu.etaxonomy.cdm.api.service.IVocabularyService;
 import eu.etaxonomy.cdm.api.service.IWorkingSetService;
+import eu.etaxonomy.cdm.api.service.molecular.IAmplificationService;
+import eu.etaxonomy.cdm.api.service.molecular.IPrimerService;
+import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
 import eu.etaxonomy.cdm.model.common.CdmBase;
 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
 import eu.etaxonomy.cdm.persistence.hibernate.permission.ICdmPermissionEvaluator;

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientClassificationService.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientClassificationService.java
index 8666796eecc064c22535b2c172e5f8b9a228d2a3..b9890789b3c4bec4e24ba9341364708ff185519d 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientClassificationService.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/dataimport/transientServices/TransientClassificationService.java
@@ -56,7 +56,7 @@ import eu.etaxonomy.cdm.strategy.merge.IMergeStrategy;
  */
 public class TransientClassificationService implements IClassificationService {
 
-    private IClassificationService defaultClassificationService;
+    private final IClassificationService defaultClassificationService;
 
     /**
      * @param defaultClassificationService
@@ -597,18 +597,6 @@ public class TransientClassificationService implements IClassificationService {
         return defaultClassificationService.countByTitle(configurator);
     }
 
-    /**
-     * @param taxon
-     * @param classification
-     * @param propertyPaths
-     * @return
-     * @see eu.etaxonomy.cdm.api.service.IClassificationService#loadChildNodesOfTaxon(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.Classification, java.util.List)
-     */
-    @Override
-    public List<TaxonNode> loadChildNodesOfTaxon(Taxon taxon, Classification classification, List<String> propertyPaths) {
-        return defaultClassificationService.loadChildNodesOfTaxon(taxon, classification, propertyPaths);
-    }
-
     /**
      * @param transientObject
      * @return
@@ -917,6 +905,15 @@ public class TransientClassificationService implements IClassificationService {
         return defaultClassificationService.findTitleCache(clazz, queryString, pageSize, pageNumber, orderHints, matchMode);
     }
 
+    /* (non-Javadoc)
+     * @see eu.etaxonomy.cdm.api.service.IClassificationService#listChildNodesOfTaxon(java.util.UUID, java.util.UUID, java.lang.Integer, java.lang.Integer, java.util.List)
+     */
+    @Override
+    public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, Integer pageSize,
+            Integer pageIndex, List<String> propertyPaths) {
+        return defaultClassificationService.listChildNodesOfTaxon(taxonUuid, classificationUuid, pageSize, pageIndex, propertyPaths);
+    }
+
 
 
 }

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/DerivateDropListener.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/DerivateDropListener.java
index 8a27c6fa7f6704c1565bfe380e5216f4c2d8e074..6f44c59435f2127bd547f8bdf2256868cec96ac9 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/DerivateDropListener.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/DerivateDropListener.java
@@ -15,9 +15,9 @@ import org.eclipse.jface.viewers.TreeNode;
 import org.eclipse.jface.viewers.ViewerDropAdapter;
 import org.eclipse.swt.dnd.TransferData;
 
-import eu.etaxonomy.cdm.api.service.IAmplificationService;
 import eu.etaxonomy.cdm.api.service.IOccurrenceService;
-import eu.etaxonomy.cdm.api.service.ISequenceService;
+import eu.etaxonomy.cdm.api.service.molecular.IAmplificationService;
+import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
 import eu.etaxonomy.cdm.model.molecular.Amplification;
 import eu.etaxonomy.cdm.model.molecular.DnaSample;
 import eu.etaxonomy.cdm.model.molecular.Sequence;