integrate trunk to branch (Taxeditor)

diff --git a/eu.etaxonomy.taxeditor.cdmlib/.classpath b/eu.etaxonomy.taxeditor.cdmlib/.classpath
index af0efc67df166667c4bce46d7e1a60695ebbf587..d1a4d25439787d1bbc7147780b4d901827010970 100644 (file)
--- a/eu.etaxonomy.taxeditor.cdmlib/.classpath
+++ b/eu.etaxonomy.taxeditor.cdmlib/.classpath
@@ -1,120 +1,120 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
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-       <classpathentry exported="true" kind="lib" path="lib/cglib-2.1.3.jar"/>
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-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>\r
+<classpath>\r
+       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>\r
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+       <classpathentry exported="true" kind="lib" path="lib/asm.jar"/>\r
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+       <classpathentry exported="true" kind="lib" path="lib/aspectjweaver-1.6.3.jar"/>\r
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+       <classpathentry exported="true" kind="lib" path="lib/hibernate-commons-annotations-3.4.0-SNAPSHOT.jar" sourcepath="lib/hibernate-commons-annotations-3.4.0-SNAPSHOTsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/hibernate-core-3.4.0-SNAPSHOT.jar" sourcepath="lib/hibernate-core-3.4.0-SNAPSHOTsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/hibernate-search-3.1.0.GA.jar" sourcepath="lib/hibernate-search-3.1.0.GAsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/hibernate-tools-3.2.0.ga.jar"/>\r
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+       <classpathentry exported="true" kind="lib" path="lib/hsqldb.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/httpclient-4.0.1.jar" sourcepath="lib/httpclient-4.0.1src.zip"/>\r
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+       <classpathentry exported="true" kind="lib" path="lib/jaxb-api-2.1.6.jar"/>\r
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+       <classpathentry exported="true" kind="lib" path="lib/jdbc-1.2.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/jdbc2_0-stdext.jar"/>\r
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+       <classpathentry exported="true" kind="lib" path="lib/joda-time-1.5.jar" sourcepath="lib/joda-time-1.5src.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/joda-time-hibernate-1.0.jar"/>\r
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+       <classpathentry exported="true" kind="lib" path="lib/jsr250-api-1.0.jar" sourcepath="lib/jsr250-api-1.0src.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/jta.jar"/>\r
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+       <classpathentry exported="true" kind="lib" path="lib/lsid-client-1.1.2.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/lsid-server-1.1.2.jar"/>\r
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+       <classpathentry exported="true" kind="lib" path="lib/lucene-spellchecker-2.4.0.jar" sourcepath="lib/lucene-spellchecker-2.4.0src.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/mail-1.4.jar" sourcepath="lib/mail-1.4src.zip"/>\r
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+       <classpathentry exported="true" kind="lib" path="lib/org.apache.commons.codec-1.3.0.jar"/>\r
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+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.aop-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.aop-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.asm-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.asm-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.aspects-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.aspects-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.beans-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.beans-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.context-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.context-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.context.support-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.context.support-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.core-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.core-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.expression-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.expression-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.jdbc-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.jdbc-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.orm-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.orm-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.oxm-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.oxm-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.transaction-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.transaction-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.web-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.web-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/org.springframework.web.servlet-3.0.4.RELEASE.jar" sourcepath="lib/org.springframework.web.servlet-3.0.4.RELEASEsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/poi-3.6.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/postgresql-8.2-504.jdbc4.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/sanselan-0.97-incubator.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/saxon9he.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/serializer-2.7.0.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/servlet-2.5.0.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/servlet-api-2.5.jar" sourcepath="lib/servlet-api-2.5src.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/slf4j-api-1.5.2.jar" sourcepath="lib/slf4j-api-1.5.2src.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/slf4j-log4j12-1.5.2.jar" sourcepath="lib/slf4j-log4j12-1.5.2src.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/spring-modules-cache-0.7.jar" sourcepath="lib/spring-modules-cache-0.7src.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/spring-modules-lucene-0.8a.jar" sourcepath="lib/spring-modules-lucene-0.8asrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/spring-security-config-3.0.5.RELEASE.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/spring-security-core-3.0.5.RELEASE.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/wsdl4j-1.6.1.jar" sourcepath="lib/wsdl4j-1.6.1src.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/xalan-2.7.0.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/xercesImpl-2.7.1.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/xercesImpl.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/xml-apis-1.3.04.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/xml-apis-ext-1.3.04.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/xml-apis.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/xml-resolver-1.2.jar" sourcepath="lib/xml-resolver-1.2src.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/xmlgraphics-commons-1.3.1.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/xom-1.0.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/xsltc.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/xstream-1.3.1.jar" sourcepath="lib/xstream-1.3.1src.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/hibernate-envers-3.4.0-SNAPSHOT.jar" sourcepath="lib/hibernate-envers-3.4.0-SNAPSHOTsrc.zip"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/spring-xml-1.5.6.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-commons-3.0.12-SNAPSHOT.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-3.0.12-SNAPSHOT.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-io-3.0.12-SNAPSHOT.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.0.12-SNAPSHOT.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-3.0.12-SNAPSHOT.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-print-3.0.12-SNAPSHOT.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-3.0.12-SNAPSHOT.jar"/>\r
+       <classpathentry exported="true" kind="lib" path="lib/cdmlib-services-3.0.12-SNAPSHOT.jar"/>\r
+       <classpathentry kind="output" path="target/classes"/>\r
+</classpath>\r

diff --git a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/selection/NamedAreaSelectionDialog.java b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/selection/NamedAreaSelectionDialog.java
index a57cbc7dff8ed3281b55b7e9f169c881257c43da..cf39589ad5b5d0257308742ac2ce10faa265d947 100644 (file)
--- a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/selection/NamedAreaSelectionDialog.java
+++ b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/dialog/selection/NamedAreaSelectionDialog.java
@@ -169,7 +169,14 @@ public class NamedAreaSelectionDialog extends
        /** {@inheritDoc} */
        @Override
        protected String getTitle(NamedArea namedArea) {
-               return NamedArea.labelWithLevel(namedArea, CdmStore.getDefaultLanguage());
+               try {
+                       String result = NamedArea.labelWithLevel(namedArea, CdmStore.getDefaultLanguage());
+                       return result;
+               } catch (Exception e) {
+                       //TODO still need to learn how errors are handled in the Tax Editor
+                       System.out.println("Error occurred when trying retrieve title for Named Area: " + namedArea.getUuid());
+                       return namedArea.getTitleCache();
+               }
        }
        
        /** {@inheritDoc} */

diff --git a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/name/ProtologueSection.java b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/name/ProtologueSection.java
index 4f4e24f5f651787624160966e96b9ab3cbc62f35..f9401eeee53caef77e05d91de846df7f47641399 100644 (file)
--- a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/name/ProtologueSection.java
+++ b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/name/ProtologueSection.java
@@ -10,7 +10,9 @@
 
 package eu.etaxonomy.taxeditor.ui.section.name;
 
+import java.util.ArrayList;
 import java.util.Collection;
+import java.util.List;
 
 import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
@@ -58,9 +60,14 @@ public class ProtologueSection extends AbstractEntityCollectionSection<TaxonName
 
        /** {@inheritDoc} */
        @Override
-       public Collection<DescriptionElementBase> getCollection(
-                       TaxonNameBase entity) {
-               return getTaxonNameDescription(entity).getElements();
+       public Collection<DescriptionElementBase> getCollection(TaxonNameBase entity) {
+               Collection<DescriptionElementBase> result = new ArrayList<DescriptionElementBase>();
+               List<TaxonNameDescription> descriptions = getTaxonNameDescriptions(entity);
+               for (TaxonNameDescription desc : descriptions){
+                       result.addAll(desc.getElements());
+               }
+               return result;
+//OLD: return getTaxonNameDescription(entity).getElements();
        }
 
 
@@ -80,13 +87,17 @@ public class ProtologueSection extends AbstractEntityCollectionSection<TaxonName
        /** {@inheritDoc} */
        @Override
        public void addElement(DescriptionElementBase element) {
+               //for simplification we always use the first description to add elements here
                getTaxonNameDescription(getEntity()).addElement(element);
        }
 
        /** {@inheritDoc} */
        @Override
        public void removeElement(DescriptionElementBase element) {
-               getTaxonNameDescription(getEntity()).removeElement(element);
+               List<TaxonNameDescription> descriptions = getTaxonNameDescriptions(getEntity());
+               for (TaxonNameDescription desc : descriptions){
+                       desc.removeElement(element);
+               } 
        }
 
        /** {@inheritDoc} */
@@ -96,13 +107,33 @@ public class ProtologueSection extends AbstractEntityCollectionSection<TaxonName
                setEntity(name);
        }
        
+       /**
+        * NOTE: returns first description
+        * @param name
+        * @return
+        */
        private TaxonNameDescription getTaxonNameDescription(TaxonNameBase name){
-               // FIXME does not handle multiple name descriptions at the moment
                if(name.getDescriptions().size() == 0){
                        name.addDescription(TaxonNameDescription.NewInstance(name));
                }
                return (TaxonNameDescription) name.getDescriptions().iterator().next();
        }
+       
+       /**
+        * Try to fix FIXME in {@link #getTaxonNameDescription(TaxonNameBase)}
+        * @param name
+        * @return
+        */
+       private List<TaxonNameDescription> getTaxonNameDescriptions(TaxonNameBase<?,?> name){
+               List<TaxonNameDescription> result = new ArrayList<TaxonNameDescription>();
+               if(name.getDescriptions().size() == 0){
+                       name.addDescription(TaxonNameDescription.NewInstance(name));
+               }
+               for (TaxonNameDescription desc : name.getDescriptions()){
+                       result.add(desc);
+               }
+               return result;
+       }
 
        /* (non-Javadoc)
         * @see eu.etaxonomy.taxeditor.section.ITaxonDetailSection#getTaxon(eu.etaxonomy.cdm.model.taxon.TaxonBase)

diff --git a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/DerivedUnitBaseDetailElement.java b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/DerivedUnitBaseDetailElement.java
index 8422ed5d958656970fb44e6c26698f2738505a55..1569bc08eb3467d5abbece97c0e85d93f9f332dd 100644 (file)
--- a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/DerivedUnitBaseDetailElement.java
+++ b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/DerivedUnitBaseDetailElement.java
@@ -41,7 +41,7 @@ public class DerivedUnitBaseDetailElement extends
 
        private TextWithLabelElement text_derivedUnitDefinitions;
 
-       private TextWithLabelElement text_accessionNumber;
+       private TextWithLabelElement text_barcode;
 
        private TextWithLabelElement text_catalogNumber;
 
@@ -82,9 +82,8 @@ public class DerivedUnitBaseDetailElement extends
                // "Specimen Definition",
                // facade.getDerivedUnitDefinition(CdmStore.getDefaultLanguage()),
                // style);
-               text_accessionNumber = formFactory.createTextWithLabelElement(
-                               formElement, "Accession Number", entity.getAccessionNumber(),
-                               style);
+               text_barcode = formFactory.createTextWithLabelElement(formElement,
+                               "Barcode", entity.getBarcode(), style);
                text_catalogNumber = formFactory
                                .createTextWithLabelElement(formElement, "Catalog Number",
                                                entity.getCatalogNumber(), style);
@@ -134,8 +133,8 @@ public class DerivedUnitBaseDetailElement extends
                        getEntity().addDerivedUnitDefinition(
                                        text_derivedUnitDefinitions.getText(),
                                        CdmStore.getDefaultLanguage());
-               } else if (eventSource == text_accessionNumber) {
-                       getEntity().setAccessionNumber(text_accessionNumber.getText());
+               } else if (eventSource == text_barcode) {
+                       getEntity().setBarcode(text_barcode.getText());
                } else if (eventSource == text_catalogNumber) {
                        getEntity().setCatalogNumber(text_catalogNumber.getText());
                } else if (eventSource == combo_preservationMethod) {

diff --git a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/GeneralDetailElement.java b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/GeneralDetailElement.java
index 5951b23dbd878800e94853747e7b0ef71896c146..30f43dd00f4dad403647906fbbcb280a36ee594c 100644 (file)
--- a/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/GeneralDetailElement.java
+++ b/eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/GeneralDetailElement.java
@@ -44,7 +44,7 @@ public class GeneralDetailElement extends
        private EntitySelectionElement<AgentBase> selection_collector;
        private TextWithLabelElement text_collectingNumber;
        private EntitySelectionElement<Collection> selection_collection;
-       private TextWithLabelElement text_barcode;
+       private TextWithLabelElement text_accessionNumber;
 
        /**
         * @param formFactory
@@ -94,8 +94,10 @@ public class GeneralDetailElement extends
                                                getConversationHolder(), formElement, "Collection",
                                                entity.getCollection(),
                                                EntitySelectionElement.ALL, style);
-               text_barcode = formFactory.createTextWithLabelElement(formElement,
-                               "Barcode", entity.getBarcode(), style);
+               text_accessionNumber = formFactory.createTextWithLabelElement(
+                               formElement, "Accession Number", entity.getAccessionNumber(),
+                               style);
+               
        }
 
        /*
@@ -127,8 +129,8 @@ public class GeneralDetailElement extends
                        getEntity().setFieldNumber(text_collectingNumber.getText());
                } else if (eventSource == selection_collection) {
                        getEntity().setCollection(selection_collection.getSelection());
-               } else if (eventSource == text_barcode) {
-                       getEntity().setBarcode(text_barcode.getText());
+               } else if (eventSource == text_accessionNumber) {
+                       getEntity().setAccessionNumber(text_accessionNumber.getText());
                }
 
                if (eventSource != toggleableText_titleCache) {