merge from trunk
authorCherian Mathew <c.mathew@bgbm.org>
Tue, 11 Feb 2014 15:30:51 +0000 (15:30 +0000)
committerCherian Mathew <c.mathew@bgbm.org>
Tue, 11 Feb 2014 15:30:51 +0000 (15:30 +0000)
13 files changed:
1  2 
eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/handler/DeleteHandler.java
eu.etaxonomy.taxeditor.cdmlib/META-INF/MANIFEST.MF
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/DeleteNodeOperation.java
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/operation/DeleteSynonymOperation.java
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/operation/DeleteTaxonOperation.java
eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/NavigationUtil.java
eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/operation/DeleteOperation.java
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/io/AbstractIOManager.java
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/io/ExportManager.java
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/io/ImportManager.java
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/ExternalReferenceServiceWizardPage.java
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/parser/ParseHandler.java
eu.etaxonomy.taxeditor.store/src/main/resources/eu/etaxonomy/cdm/editorApplicationContext.xml

index f08c60f92954a3edc7d4aaa0a1e212547b988190,f08c60f92954a3edc7d4aaa0a1e212547b988190..eb74e5e7504d89fc8c7a57738ac4b4f27fe61207
@@@ -20,12 -20,12 +20,12 @@@ import org.eclipse.ui.IEditorPart
  import org.eclipse.ui.handlers.HandlerUtil;
  import org.eclipse.ui.texteditor.IDocumentProvider;
  
--import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  import eu.etaxonomy.cdm.api.service.IOccurrenceService;
  import eu.etaxonomy.cdm.api.service.IReferenceService;
  import eu.etaxonomy.cdm.api.service.ITaxonService;
  import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  import eu.etaxonomy.cdm.model.reference.Reference;
++import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  import eu.etaxonomy.taxeditor.annotatedlineeditor.IEntityPersistenceService;
  import eu.etaxonomy.taxeditor.annotatedlineeditor.LineAnnotation;
@@@ -73,8 -73,8 +73,8 @@@ public class DeleteHandler extends Abst
                                        LineAnnotation annotation = (LineAnnotation) model.getAnnotation(object);
                                                        
                                        try {
--                                              CdmApplicationController controller;
--                                              controller = (CdmApplicationController) CdmStore.getCurrentApplicationConfiguration();
++                                              ICdmApplicationConfiguration controller;
++                                              controller = (ICdmApplicationConfiguration) CdmStore.getCurrentApplicationConfiguration();
                                                //persistenceService.delete(object);
                                                if (object instanceof SpecimenOrObservationBase){
                                                        
index fa2153544aad4f01f6b976f205dd2fb13393b25d,9a498aca84582754759d372d6e38f57016241cd9..264bcaaff6a68b62c3f66cd94856652abad068db
@@@ -123,7 -123,6 +123,7 @@@ Export-Package: com.google.api
   eu.etaxonomy.cdm.print.out.pdf,
   eu.etaxonomy.cdm.print.out.taxpub,
   eu.etaxonomy.cdm.print.out.xml,
 + eu.etaxonomy.cdm.remote.api.application,
   eu.etaxonomy.cdm.remote.config,
   eu.etaxonomy.cdm.remote.controller,
   eu.etaxonomy.cdm.remote.controller.csv,
   org.springframework.security.core.context,
   org.springframework.security.core.userdetails,
   org.springframework.security.provisioning,
 + org.springframework.security.remoting.httpinvoker,
   org.springframework.stereotype,
   org.springframework.transaction;uses:="org.springframework.core",
   org.springframework.transaction.annotation;uses:="javax.ejb,org.springframework.transaction.interceptor",
@@@ -594,5 -592,4 +594,6 @@@ Bundle-ClassPath: .
   lib/yjp-controller-api-redist-9.0.8.jar,
   lib/google-api-translate-java-0.92.jar,
   lib/odfdom-0.8.jar,
 - lib/h2mig_pagestore_addon.jar
 + lib/h2mig_pagestore_addon.jar,
 + lib/spring-security-remoting-3.1.3.RELEASE.jar
++Import-Package: eu.etaxonomy.cdm.api.application
index 25bef92d7760429f17f85696e4c2ddcd2e1cf151,db6aa6c8e2fd275ff39cad1bc5579a46a0519900..9b3b1ada9941074997befda33422d1f7825a9cb9
@@@ -8,11 -8,13 +8,13 @@@ import org.eclipse.core.commands.operat
  import org.eclipse.core.runtime.IAdaptable;
  import org.eclipse.core.runtime.IProgressMonitor;
  import org.eclipse.core.runtime.IStatus;
+ import org.eclipse.jface.dialogs.MessageDialog;
+ import org.eclipse.ui.handlers.HandlerUtil;
  
--import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  import eu.etaxonomy.cdm.api.service.IPolytomousKeyNodeService;
  import eu.etaxonomy.cdm.api.service.ITaxonService;
  import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;
++import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  import eu.etaxonomy.taxeditor.operation.AbstractPostOperation;
  import eu.etaxonomy.taxeditor.operation.IPostOperationEnabled;
  import eu.etaxonomy.taxeditor.store.CdmStore;
@@@ -43,16 -45,20 +45,20 @@@ public class DeleteNodeOperation extend
        @Override
        public IStatus execute(IProgressMonitor monitor, IAdaptable info)
                        throws ExecutionException {
+               
                //parent.removeChild(node);
--              CdmApplicationController controller;
++              ICdmApplicationConfiguration controller;
                
--              controller = (CdmApplicationController) CdmStore.getCurrentApplicationConfiguration();
++              controller = (ICdmApplicationConfiguration) CdmStore.getCurrentApplicationConfiguration();
                
                IPolytomousKeyNodeService service = controller.getPolytomousKeyNodeService();
-               
-               service.delete(node, true);
+               if (node.getChildren().size()>0){
+                       if(! MessageDialog.openQuestion(null, "Confirm deletion of children", "The selected node has children, do you want to delete them, too?")) {
+                               service.delete(node, false);
+                       }
+               } else{
+                       service.delete(node, true);
+               }
                return postExecute(null);
        }
  
index 76e1b34f844e661a9c7cd5cfe02a3557055d6ace,76e1b34f844e661a9c7cd5cfe02a3557055d6ace..159840d6531da0917db99d22f394842d580dc5ef
@@@ -17,11 -17,11 +17,11 @@@ import org.eclipse.core.runtime.IAdapta
  import org.eclipse.core.runtime.IProgressMonitor;
  import org.eclipse.core.runtime.IStatus;
  
--import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  import eu.etaxonomy.cdm.api.service.ITaxonService;
  import eu.etaxonomy.cdm.model.taxon.Synonym;
  import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  import eu.etaxonomy.cdm.model.taxon.Taxon;
++import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  import eu.etaxonomy.taxeditor.operation.AbstractPostOperation;
  import eu.etaxonomy.taxeditor.operation.IPostOperationEnabled;
  import eu.etaxonomy.taxeditor.store.CdmStore;
@@@ -67,9 -67,9 +67,9 @@@ public class DeleteSynonymOperation ext
                                
                                // Remove synonym from taxon
                                
--                              CdmApplicationController controller;
++                              ICdmApplicationConfiguration controller;
                                
--                              controller = (CdmApplicationController) CdmStore.getCurrentApplicationConfiguration();
++                              controller = (ICdmApplicationConfiguration) CdmStore.getCurrentApplicationConfiguration();
                                
                                ITaxonService service = controller.getTaxonService();
                                if (synonym.getId() == 0){
index b1a365900c94e0b47157a72dc218af4ec425625d,b1a365900c94e0b47157a72dc218af4ec425625d..ddc6e90bae234be2bb592e12da344646ecced197
@@@ -19,7 -19,7 +19,6 @@@ import org.eclipse.ui.IWorkbenchPage
  import org.eclipse.ui.PartInitException;\r
  import org.eclipse.ui.handlers.HandlerUtil;\r
  \r
--import eu.etaxonomy.cdm.api.application.CdmApplicationController;\r
  import eu.etaxonomy.cdm.api.conversation.IConversationEnabled;\r
  import eu.etaxonomy.cdm.api.service.ITaxonService;\r
  import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;\r
@@@ -28,6 -28,6 +27,7 @@@ import eu.etaxonomy.cdm.model.taxon.Cla
  import eu.etaxonomy.cdm.model.taxon.Synonym;\r
  import eu.etaxonomy.cdm.model.taxon.Taxon;\r
  import eu.etaxonomy.cdm.model.taxon.TaxonNode;\r
++import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;\r
  import eu.etaxonomy.taxeditor.editor.TaxonEditorInput;\r
  import eu.etaxonomy.taxeditor.operation.AbstractPostOperation;\r
  import eu.etaxonomy.taxeditor.operation.IPostOperationEnabled;\r
@@@ -73,9 -73,9 +73,9 @@@ public class DeleteTaxonOperation exten
                                bind();\r
                                \r
                                \r
--                              CdmApplicationController controller;\r
++                              ICdmApplicationConfiguration controller;\r
                                \r
--                              controller = (CdmApplicationController) CdmStore.getCurrentApplicationConfiguration();\r
++                              controller = (ICdmApplicationConfiguration) CdmStore.getCurrentApplicationConfiguration();\r
                                \r
                                ITaxonService service = controller.getTaxonService();\r
                                try {\r
index 9fdb66b7acb266a0dcae034a2c7766d74e3b7150,9fdb66b7acb266a0dcae034a2c7766d74e3b7150..db12603068cb6d992b1ee67e4379c0d78066cd96
@@@ -98,6 -98,6 +98,7 @@@ public class NavigationUtil extends Abs
                        AbstractUtility.error(NavigationUtil.class, "Error opening the editor", e);
                } catch (Exception e) {
                        AbstractUtility.warningDialog("Could not create Taxon", NavigationUtil.class, e.getMessage());
++                      e.printStackTrace();
                }
        }
  
index 9cd017a222c44819d6cbb38fbc6bc7dcd39ec05a,9cd017a222c44819d6cbb38fbc6bc7dcd39ec05a..d1737c14e031f03117b88f8bdb0989d60d33edef
@@@ -20,8 -20,8 +20,6 @@@ import org.eclipse.core.runtime.IStatus
  import org.eclipse.jface.dialogs.MessageDialog;
  import org.eclipse.ui.handlers.HandlerUtil;
  
--import eu.etaxonomy.cdm.api.application.CdmApplicationController;
--import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  import eu.etaxonomy.cdm.api.conversation.IConversationEnabled;
  import eu.etaxonomy.cdm.api.service.IClassificationService;
  import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
@@@ -34,6 -34,6 +32,8 @@@ import eu.etaxonomy.cdm.model.common.IT
  import eu.etaxonomy.cdm.model.taxon.Classification;
  import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
  import eu.etaxonomy.cdm.model.taxon.TaxonNode;
++import eu.etaxonomy.cdm.api.application.CdmApplicationController;
++import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  import eu.etaxonomy.taxeditor.operation.AbstractPersistentPostOperation;
  import eu.etaxonomy.taxeditor.operation.IPostOperationEnabled;
  import eu.etaxonomy.taxeditor.store.CdmStore;
index 5b0d4fc6f1e2a33805ca03c3c93bab1f6fc58fb7,5b0d4fc6f1e2a33805ca03c3c93bab1f6fc58fb7..6bc1250bcbcac995634141f1b4c863127ec64c9f
@@@ -13,8 -13,8 +13,8 @@@ package eu.etaxonomy.taxeditor.io
  import org.eclipse.core.runtime.jobs.Job;
  import org.eclipse.ui.progress.IProgressConstants;
  
--import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  import eu.etaxonomy.cdm.io.common.IIoConfigurator;
++import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  
  /**
   * <p>
@@@ -40,7 -40,7 +40,7 @@@ public abstract class AbstractIOManager
         * 
         * @param applicationController
         *            a
--       *            {@link eu.etaxonomy.cdm.api.application.CdmApplicationController}
++       *            {@link eu.etaxonomy.cdm.remote.api.application.CdmApplicationController}
         *            object.
         * @param <CONFIGURATOR>
         *            a CONFIGURATOR object.
index 984b7697b94aec721f63f5b821d4be9a1e55dbf8,984b7697b94aec721f63f5b821d4be9a1e55dbf8..b19810b89d7ee4b1237978fe636194ea7833569e
@@@ -18,13 -18,13 +18,13 @@@ import org.eclipse.core.runtime.jobs.Jo
  import org.eclipse.swt.widgets.Display;
  import org.eclipse.ui.IWorkbenchPart;
  
--import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  import eu.etaxonomy.cdm.api.conversation.IConversationEnabled;
  import eu.etaxonomy.cdm.io.common.CdmDefaultExport;
  import eu.etaxonomy.cdm.io.common.IExportConfigurator;
  import eu.etaxonomy.cdm.io.common.IIoConfigurator;
  import eu.etaxonomy.cdm.io.jaxb.JaxbExportConfigurator;
  import eu.etaxonomy.cdm.io.sdd.out.SDDExportConfigurator;
++import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  import eu.etaxonomy.taxeditor.model.CdmProgressMonitorAdapter;
  import eu.etaxonomy.taxeditor.store.StoreUtil;
  
@@@ -54,7 -54,7 +54,7 @@@ public class ExportManager extends Abst
         * 
         * @param applicationConfiguration
         *            a
--       *            {@link eu.etaxonomy.cdm.api.application.CdmApplicationController}
++       *            {@link eu.etaxonomy.cdm.remote.api.application.CdmApplicationController}
         *            object.
         * @return a {@link eu.etaxonomy.taxeditor.io.ExportManager} object.
         */
index 64e097cb349bda65d44fca07e5c0f1d378f50cf0,64e097cb349bda65d44fca07e5c0f1d378f50cf0..48246bfcf43c08f3ad271654c2002d6a14c72868
@@@ -17,7 -17,7 +17,6 @@@ import org.eclipse.core.runtime.Status
  import org.eclipse.core.runtime.jobs.Job;
  import org.eclipse.swt.widgets.Display;
  
--import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  import eu.etaxonomy.cdm.io.excel.taxa.NormalExplicitImportConfigurator;
@@@ -27,6 -27,6 +26,7 @@@ import eu.etaxonomy.cdm.io.sdd.in.SDDIm
  import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
  import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenCdmExcelImportConfigurator;
  import eu.etaxonomy.cdm.io.tcsxml.in.TcsXmlImportConfigurator;
++import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  import eu.etaxonomy.taxeditor.model.CdmProgressMonitorAdapter;
  import eu.etaxonomy.taxeditor.store.CdmStore;
  import eu.etaxonomy.taxeditor.store.StoreUtil;
@@@ -56,7 -56,7 +56,7 @@@ public class ImportManager extends Abst
         * 
         * @param applicationConfiguration
         *            a
--       *            {@link eu.etaxonomy.cdm.api.application.CdmApplicationController}
++       *            {@link eu.etaxonomy.cdm.remote.api.application.CdmApplicationController}
         *            object.
         * @return a {@link eu.etaxonomy.taxeditor.io.ImportManager} object.
         */
index 1348b2a67726408c713dc58abe7c7268125a5392,1348b2a67726408c713dc58abe7c7268125a5392..0ddc337cdc4414bdd2f04123c097dbf2cfc13547
@@@ -27,11 -27,11 +27,11 @@@ import org.eclipse.swt.widgets.Button
  import org.eclipse.swt.widgets.Composite;
  import org.eclipse.swt.widgets.Text;
  
--import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
  import eu.etaxonomy.cdm.ext.ipni.IIpniService;
  import eu.etaxonomy.cdm.ext.ipni.IpniService;
  import eu.etaxonomy.cdm.model.reference.Reference;
++import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
  import eu.etaxonomy.taxeditor.store.CdmStore;
  import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
  import eu.etaxonomy.taxeditor.ui.element.LayoutConstants;
index 0ca07983aaf269d2acd64d8edb7b03239c6943d6,0ca07983aaf269d2acd64d8edb7b03239c6943d6..9616b0ff6225a672da3fdf892527cc88b7e7e09b
@@@ -162,7 -162,7 +162,7 @@@ public class ParseHandler
                
                MatchMatrix matchMatrix = findMatches(parsedName);
                
--              resolveDuplicates(parsedName, matchMatrix);
++//            resolveDuplicates(parsedName, matchMatrix);
                
                return parsedName;
        }
         * @return      A <code>List</code> of possibly matching TaxonNameBase's.
         */
        private List<TaxonNameBase> findMatchingLatinNames(TaxonNameBase taxonNameBase) {
--
--              try {
--                      return CdmStore.getService(ICommonService.class).findMatching(taxonNameBase, MatchStrategyConfigurator.NonViralNameMatchStrategy());
--                      
--              } catch (MatchException e) {
--                      StoreUtil.error(this.getClass(), "Error finding matching names", e);
--              }
++//
++//            try {
++//                    return CdmStore.getService(ICommonService.class).findMatching(taxonNameBase, MatchStrategyConfigurator.NonViralNameMatchStrategy());
++//                    
++//            } catch (MatchException e) {
++//                    StoreUtil.error(this.getClass(), "Error finding matching names", e);
++//            }
                return null;
        }
  }
index 718401b9236c3ece4d72216d4a8922fbdc25a693,6c394edea6cfee96373917d4e99a0a685df16b19..eda9d21c496236d29992ff369c57c0fbdc0dd2ca
@@@ -7,16 -7,12 +7,19 @@@
      http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-2.5.xsd
      http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context-2.5.xsd">\r
  \r
 -  <import resource="classpath:/eu/etaxonomy/cdm/defaultApplicationContext.xml"/>\r
 -  <!-- <import resource="classpath:/eu/etaxonomy/cdm/remotingApplicationContext.xml"/> -->\r
 -  <bean id="persistentTermInitializer" class="eu.etaxonomy.cdm.database.PersistentTermInitializer">\r
 +  <!-- <import resource="classpath:/eu/etaxonomy/cdm/defaultApplicationContext.xml"/> -->\r
 +  <import resource="classpath:/eu/etaxonomy/cdm/remotingApplicationContext.xml"/>\r
 +  \r
 +   <!-- <bean id="persistentTermInitializer" class="eu.etaxonomy.cdm.database.PersistentTermInitializer">\r
      <property name="omit" value="false" />\r
 -  </bean>\r
 +  </bean> -->\r
 +   \r
 +  <!-- <bean id="remoteTermInitializer" class="eu.etaxonomy.cdm.remote.service.RemoteTermInitializer">    \r
 +  </bean> -->\r
    \r
++ \r
++\r
++    \r
    <import resource="classpath:/eu/etaxonomy/cdm/remote.xml"/>\r
    <import resource="classpath:eu/etaxonomy/cdm/remote/json/jsonConfigurations.xml"/>\r
    \r