eu.etaxonomy.taxeditor.store/icons/bookmark.gif -text
eu.etaxonomy.taxeditor.store/icons/category.gif -text
eu.etaxonomy.taxeditor.store/icons/change.gif -text
+eu.etaxonomy.taxeditor.store/icons/character_data_derivate-16x16-32.png -text
eu.etaxonomy.taxeditor.store/icons/clear.gif -text
eu.etaxonomy.taxeditor.store/icons/close.gif -text
eu.etaxonomy.taxeditor.store/icons/close_view.gif -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/MinMaxTextSection.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/MultilanguageTextElement.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/NumberWithLabelElement.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/OriginalLabelDataElement.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/PartialElement.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/PointElement.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/RootElement.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/AbstractCdmComposite.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/DerivedUnitGeneralDetailElementMVC.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/GeographicPointElement.java -text
-eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/OriginalLabelDataController.java -text
-eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/OriginalLabelDataElement.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/OriginalLabelDataField.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/combo/EnumTermCombo.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/combo/EnumTermComboController.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/element/DateElement.java -text
<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-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-commons-3.3.7-SNAPSHOT.jar" sourcepath="lib/cdmlib-commons-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-3.3.7-SNAPSHOT.jar" sourcepath="lib/cdmlib-ext-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-io-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-io-3.3.7-SNAPSHOT.jar" sourcepath="lib/cdmlib-io-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.3.7-SNAPSHOT.jar" sourcepath="lib/cdmlib-model-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-3.3.7-SNAPSHOT.jar" sourcepath="lib/cdmlib-persistence-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-print-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-print-3.3.7-SNAPSHOT.jar" sourcepath="lib/cdmlib-print-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-3.3.7-SNAPSHOT.jar" sourcepath="lib/cdmlib-remote-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-services-3.3.7-SNAPSHOT-sources.jar"/>
- <classpathentry exported="true" kind="lib" path="lib/cdmlib-services-3.3.7-SNAPSHOT.jar" sourcepath="lib/cdmlib-services-3.3.7-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-commons-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-commons-3.4.0-SNAPSHOT.jar" sourcepath="lib/cdmlib-commons-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-ext-3.4.0-SNAPSHOT.jar" sourcepath="lib/cdmlib-ext-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-io-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-io-3.4.0-SNAPSHOT.jar" sourcepath="lib/cdmlib-io-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-model-3.4.0-SNAPSHOT.jar" sourcepath="lib/cdmlib-model-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-persistence-3.4.0-SNAPSHOT.jar" sourcepath="lib/cdmlib-persistence-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-print-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-print-3.4.0-SNAPSHOT.jar" sourcepath="lib/cdmlib-print-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-remote-3.4.0-SNAPSHOT.jar" sourcepath="lib/cdmlib-remote-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-services-3.4.0-SNAPSHOT-sources.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/cdmlib-services-3.4.0-SNAPSHOT.jar" sourcepath="lib/cdmlib-services-3.4.0-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"/>
lib/batik-util-1.7.jar,
lib/batik-xml-1.7.jar,
lib/c3p0-0.9.2.jar,
- lib/cdmlib-commons-3.3.7-SNAPSHOT-sources.jar,
- lib/cdmlib-commons-3.3.7-SNAPSHOT.jar,
- lib/cdmlib-ext-3.3.7-SNAPSHOT-sources.jar,
- lib/cdmlib-ext-3.3.7-SNAPSHOT.jar,
- lib/cdmlib-io-3.3.7-SNAPSHOT-sources.jar,
- lib/cdmlib-io-3.3.7-SNAPSHOT.jar,
- lib/cdmlib-model-3.3.7-SNAPSHOT-sources.jar,
- lib/cdmlib-model-3.3.7-SNAPSHOT.jar,
- lib/cdmlib-persistence-3.3.7-SNAPSHOT-sources.jar,
- lib/cdmlib-persistence-3.3.7-SNAPSHOT.jar,
- lib/cdmlib-print-3.3.7-SNAPSHOT-sources.jar,
- lib/cdmlib-print-3.3.7-SNAPSHOT.jar,
- lib/cdmlib-remote-3.3.7-SNAPSHOT-sources.jar,
- lib/cdmlib-remote-3.3.7-SNAPSHOT.jar,
- lib/cdmlib-services-3.3.7-SNAPSHOT-sources.jar,
- lib/cdmlib-services-3.3.7-SNAPSHOT.jar,
lib/cglib-nodep-2.2.2.jar,
lib/com.springsource.org.aopalliance-1.0.0.jar,
lib/com.springsource.org.apache.commons.logging-1.1.1.jar,
lib/google-api-translate-java-0.92.jar,
lib/odfdom-0.8.jar,
lib/h2mig_pagestore_addon.jar,
- lib/spring-security-remoting-3.1.3.RELEASE.jar
+ lib/spring-security-remoting-3.1.3.RELEASE.jar,
+ lib/cdmlib-commons-3.4.0-SNAPSHOT-sources.jar,
+ lib/cdmlib-commons-3.4.0-SNAPSHOT.jar,
+ lib/cdmlib-ext-3.4.0-SNAPSHOT-sources.jar,
+ lib/cdmlib-ext-3.4.0-SNAPSHOT.jar,
+ lib/cdmlib-io-3.4.0-SNAPSHOT-sources.jar,
+ lib/cdmlib-io-3.4.0-SNAPSHOT.jar,
+ lib/cdmlib-model-3.4.0-SNAPSHOT-sources.jar,
+ lib/cdmlib-model-3.4.0-SNAPSHOT.jar,
+ lib/cdmlib-persistence-3.4.0-SNAPSHOT-sources.jar,
+ lib/cdmlib-persistence-3.4.0-SNAPSHOT.jar,
+ lib/cdmlib-print-3.4.0-SNAPSHOT-sources.jar,
+ lib/cdmlib-print-3.4.0-SNAPSHOT.jar,
+ lib/cdmlib-remote-3.4.0-SNAPSHOT-sources.jar,
+ lib/cdmlib-remote-3.4.0-SNAPSHOT.jar,
+ lib/cdmlib-services-3.4.0-SNAPSHOT-sources.jar,
+ lib/cdmlib-services-3.4.0-SNAPSHOT.jar
Import-Package: eu.etaxonomy.cdm.api.application
lib/batik-util-1.7.jar,\\r
lib/batik-xml-1.7.jar,\\r
lib/c3p0-0.9.2.jar,\\r
- lib/cdmlib-commons-3.3.7-SNAPSHOT-sources.jar,\\r
- lib/cdmlib-commons-3.3.7-SNAPSHOT.jar,\\r
- lib/cdmlib-ext-3.3.7-SNAPSHOT-sources.jar,\\r
- lib/cdmlib-ext-3.3.7-SNAPSHOT.jar,\\r
- lib/cdmlib-io-3.3.7-SNAPSHOT-sources.jar,\\r
- lib/cdmlib-io-3.3.7-SNAPSHOT.jar,\\r
- lib/cdmlib-model-3.3.7-SNAPSHOT-sources.jar,\\r
- lib/cdmlib-model-3.3.7-SNAPSHOT.jar,\\r
- lib/cdmlib-persistence-3.3.7-SNAPSHOT-sources.jar,\\r
- lib/cdmlib-persistence-3.3.7-SNAPSHOT.jar,\\r
- lib/cdmlib-print-3.3.7-SNAPSHOT-sources.jar,\\r
- lib/cdmlib-print-3.3.7-SNAPSHOT.jar,\\r
- lib/cdmlib-remote-3.3.7-SNAPSHOT-sources.jar,\\r
- lib/cdmlib-remote-3.3.7-SNAPSHOT.jar,\\r
- lib/cdmlib-services-3.3.7-SNAPSHOT-sources.jar,\\r
- lib/cdmlib-services-3.3.7-SNAPSHOT.jar,\\r
lib/cglib-nodep-2.2.2.jar,\\r
lib/com.springsource.org.aopalliance-1.0.0.jar,\\r
lib/com.springsource.org.apache.commons.logging-1.1.1.jar,\\r
lib/google-api-translate-java-0.92.jar,\\r
lib/odfdom-0.8.jar,\\r
lib/h2mig_pagestore_addon.jar,\\r
- lib/spring-security-remoting-3.1.3.RELEASE.jar\r
+ lib/spring-security-remoting-3.1.3.RELEASE.jar,\\r
+ lib/cdmlib-commons-3.4.0-SNAPSHOT-sources.jar,\\r
+ lib/cdmlib-commons-3.4.0-SNAPSHOT.jar,\\r
+ lib/cdmlib-ext-3.4.0-SNAPSHOT-sources.jar,\\r
+ lib/cdmlib-ext-3.4.0-SNAPSHOT.jar,\\r
+ lib/cdmlib-io-3.4.0-SNAPSHOT-sources.jar,\\r
+ lib/cdmlib-io-3.4.0-SNAPSHOT.jar,\\r
+ lib/cdmlib-model-3.4.0-SNAPSHOT-sources.jar,\\r
+ lib/cdmlib-model-3.4.0-SNAPSHOT.jar,\\r
+ lib/cdmlib-persistence-3.4.0-SNAPSHOT-sources.jar,\\r
+ lib/cdmlib-persistence-3.4.0-SNAPSHOT.jar,\\r
+ lib/cdmlib-print-3.4.0-SNAPSHOT-sources.jar,\\r
+ lib/cdmlib-print-3.4.0-SNAPSHOT.jar,\\r
+ lib/cdmlib-remote-3.4.0-SNAPSHOT-sources.jar,\\r
+ lib/cdmlib-remote-3.4.0-SNAPSHOT.jar,\\r
+ lib/cdmlib-services-3.4.0-SNAPSHOT-sources.jar,\\r
+ lib/cdmlib-services-3.4.0-SNAPSHOT.jar\r
jars.compile.order = .\r
output.. = bin/\r
source.. = src/main/java/,\\r
import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
import eu.etaxonomy.taxeditor.editor.EditorUtil;
+import eu.etaxonomy.taxeditor.model.AbstractUtility;
import eu.etaxonomy.taxeditor.store.CdmStore;
public class DataImportEditorContextMenu extends CompoundContributionItem {
@Override
public void fill(Menu menu, int index) {
final IWorkbenchWindow window = PlatformUI.getWorkbench().getActiveWorkbenchWindow();
- final IEditorPart activeEditor = window.getActivePage().getActiveEditor();
+ final IEditorPart activeEditor = AbstractUtility.getActiveEditor();
final ISelection selection = window.getActivePage().getSelection();
if(selection instanceof StructuredSelection){
final StructuredSelection structuredSelection = (StructuredSelection)selection;
import eu.etaxonomy.cdm.api.service.IOccurrenceService;
import eu.etaxonomy.cdm.api.service.config.DeleteConfiguratorBase;
import eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator;
+import eu.etaxonomy.cdm.api.service.dto.DerivateHierarchyDTO;
import eu.etaxonomy.cdm.api.service.pager.Pager;
import eu.etaxonomy.cdm.api.service.search.SearchResult;
import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
return defaultService.findWithoutFlush(uuid);
}
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listFieldUnitsByAssociatedTaxon(java.util.Set, eu.etaxonomy.cdm.model.taxon.Taxon, java.lang.Integer, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
+ */
+ @Override
+ public Collection<FieldUnit> listFieldUnitsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,
+ Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
+ List<String> propertyPaths) {
+ return defaultService.listFieldUnitsByAssociatedTaxon(includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths);
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDerivateHierarchyDTOsByAssociatedTaxon(java.util.Set, eu.etaxonomy.cdm.model.taxon.Taxon, java.lang.Integer, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
+ */
+ @Override
+ public Collection<DerivateHierarchyDTO> listDerivateHierarchyDTOsByAssociatedTaxon(
+ Set<TaxonRelationshipEdge> includeRelationships, Taxon associatedTaxon, Integer maxDepth, Integer pageSize,
+ Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
+ return defaultService.listDerivateHierarchyDTOsByAssociatedTaxon(includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths);
+ }
+
}
import org.eclipse.jface.viewers.AbstractTreeViewer;
import org.eclipse.jface.viewers.StructuredSelection;
import org.eclipse.jface.viewers.TreeNode;
+import org.eclipse.jface.viewers.TreeSelection;
import org.eclipse.jface.viewers.TreeViewer;
import org.eclipse.swt.SWT;
import org.eclipse.swt.dnd.DND;
import org.eclipse.ui.IEditorInput;
import org.eclipse.ui.IEditorPart;
import org.eclipse.ui.IEditorSite;
-import org.eclipse.ui.IMemento;
import org.eclipse.ui.PartInitException;
import org.eclipse.ui.part.EditorPart;
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
import eu.etaxonomy.cdm.persistence.hibernate.CdmDataChangeMap;
-import eu.etaxonomy.taxeditor.model.IContextListener;
import eu.etaxonomy.taxeditor.model.IDirtyMarkableSelectionProvider;
import eu.etaxonomy.taxeditor.model.IPartContentHasDetails;
import eu.etaxonomy.taxeditor.model.IPartContentHasFactualData;
*
*/
public class DerivateView extends EditorPart implements IPartContentHasFactualData, IDirtyMarkableSelectionProvider,
- IConversationEnabled, IPartContentHasDetails, IPartContentHasSupplementalData, IContextListener {
+ IConversationEnabled, IPartContentHasDetails, IPartContentHasSupplementalData {
/**
* Key used for storing a single DerivateView in a memento
* Default constructor
*/
public DerivateView() {
- CdmStore.getContextManager().addContextListener(this);
}
/* (non-Javadoc)
viewer.refresh();
}
+ /**
+ * Refreshes the derivate hierarchy tree and expands the tree
+ * to show and select the given object.
+ *
+ * @param expandTo the object to which the tree should be expanded
+ */
+ public void refreshTree(Object expandTo){
+ refreshTree();
+ TreeSelection selection = (TreeSelection) viewer.getSelection();
+ viewer.expandToLevel(selection.getFirstElement(), 1);
+ viewer.setSelection(new StructuredSelection(new TreeNode(expandTo)));
+ }
+
/**
* Refreshes the derivate hierarchy tree
*/
viewer.refresh();
}
+
private void generateMultiLinkSingleReads() {
Set<SingleRead> multiLinkSingleReads = new HashSet<SingleRead>();
for(Entry<SingleRead, Collection<Sequence>> entry:CdmStore.getService(ISequenceService.class).getSingleReadSequencesMap().entrySet()){
return this.multiLinkSingleReads;
}
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.model.IContextListener#contextAboutToStop(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor)
- */
- @Override
- public void contextAboutToStop(IMemento memento, IProgressMonitor monitor) {
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.model.IContextListener#contextStop(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor)
- */
- @Override
- public void contextStop(IMemento memento, IProgressMonitor monitor) {
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.model.IContextListener#contextStart(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor)
- */
- @Override
- public void contextStart(IMemento memento, IProgressMonitor monitor) {
-// if(memento == null){
-// return;
-// }
-// IMemento editorMementos = memento.getChild(DERIVATE_VIEW_MEMENTO_KEY);
-// DerivateViewEditorInput input = new DerivateViewEditorInput(UUID.fromString(editorInput.getString(DerivateViewEditorInput.UUID_MEMENTO_KEY)));
-// try {
-// EditorUtil.open(input);
-// } catch (PartInitException e) {
-// AbstractUtility.error(getClass(), "Error opening an editor window", e);
-// }
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.model.IContextListener#contextRefresh(org.eclipse.core.runtime.IProgressMonitor)
- */
- @Override
- public void contextRefresh(IProgressMonitor monitor) {
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.model.IContextListener#workbenchShutdown(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor)
- */
- @Override
- public void workbenchShutdown(IMemento memento, IProgressMonitor monitor) {
-// if (!conversation.isBound()) {
-// conversation.bind();
-// }
-// conversation.close();
-// if(memento == null){
-// return;
-// }
-//
-// IEditorInput input = getEditorInput();
-// if(input instanceof IPersistable){
-// memento.createChild(DERIVATE_VIEW_MEMENTO_KEY);
-// ((IPersistable) input).saveState(memento);
-// }
- }
-
}
//context menu for TissueSample
else if(selectedTreeNode.getValue() instanceof DerivedUnit && ((DerivedUnit)selectedTreeNode.getValue()).getRecordBasis()==SpecimenOrObservationType.TissueSample){
createMenuItem(addMenu, "DnaSample", selectedTreeNode, DnaSample.class, null);
+ createMenuItem(addMenu, "Media Specimen", selectedTreeNode, MediaSpecimen.class, SpecimenOrObservationType.Media);
}
//context menu for DnaSample
else if(selectedTreeNode.getValue() instanceof DnaSample){
createMenuItem(addMenu, "Consensus Sequence", selectedTreeNode, Sequence.class, null);
+ createMenuItem(addMenu, "Media Specimen", selectedTreeNode, MediaSpecimen.class, SpecimenOrObservationType.Media);
}
//context menu for Sequence
else if(selectedTreeNode.getValue() instanceof Sequence){
*/
@Override
public void widgetSelected(SelectionEvent e) {
+ Object createdElement = null;
Object selectedDerivate = selectedNode.getValue();
if(selectedDerivate instanceof DnaSample){
DnaSample dnaSample = (DnaSample)selectedDerivate;
if(childClass.equals(Sequence.class)){
- dnaSample.addSequence(Sequence.NewInstance(""));//why does this not have DnaSample as constructor parameter?
+ Sequence newInstance = Sequence.NewInstance("");
+ dnaSample.addSequence(newInstance);//why does this not have DnaSample as constructor parameter?
+ createdElement = newInstance;
}
}
else if(selectedDerivate instanceof Sequence){
- ((Sequence) selectedDerivate).addSingleRead(SingleRead.NewInstance());
+ SingleRead newInstance = SingleRead.NewInstance();
+ ((Sequence) selectedDerivate).addSingleRead(newInstance);
+ createdElement = newInstance;
}
else if(selectedDerivate instanceof SpecimenOrObservationBase && DerivedUnit.class.isAssignableFrom(childClass)){
SpecimenOrObservationBase<?> specimenOrObservationBase = (SpecimenOrObservationBase<?>)selectedDerivate;
specimenOrObservationBase.addDerivationEvent(DerivationEvent.NewSimpleInstance(specimenOrObservationBase, derivedUnit, DerivationEventType.GATHERING_IN_SITU()));
derivedUnit.setCacheStrategy(new DerivedUnitFacadeCacheStrategy());
derivedUnit.getTitleCache(); //update title cache
+ createdElement = derivedUnit;
}
//refresh view
if(activePart instanceof DerivateView){
DerivateView derivateView = (DerivateView)activePart;
derivateView.changed(null);
- derivateView.refreshTree();
+ derivateView.refreshTree(createdElement);
}
}
}
<?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"/>
<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
<classpathentry including="**/*.java" kind="src" path="src/main/java"/>
<classpathentry including="**/*.java" kind="src" path="src/test/java"/>
<classpathentry kind="src" path="src/main/resources"/>
<classpathentry including="**/*.java" kind="src" path="src/test/resources"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="output" path="target/classes"/>
</classpath>
org.eclipse.jface.text,
org.eclipse.ui.forms,
eu.etaxonomy.taxeditor.cdmlib,
- org.eclipse.nebula.widgets.compositetable;bundle-version="1.0.0"
+ org.eclipse.nebula.widgets.compositetable;bundle-version="1.0.0",
+ org.eclipse.core.databinding,
+ org.eclipse.core.databinding.beans,
+ org.eclipse.core.databinding.observable,
+ org.eclipse.core.databinding.property,
+ org.eclipse.jface.databinding
Import-Package: org.eclipse.core.commands,
org.eclipse.core.commands.operations,
org.eclipse.core.expressions,
public static final String SINGLE_READ_DERIVATE = "single_read_derivate";
public static final String SINGLE_READ_DERIVATE_MULTILINK = "single_read_derivate_multilink";
+ public static final String CHARACTER_DATA_DERIVATE = "character_data_derivate";
+
/***************************************************************************
"single_read_derivate-16x16-32.png");
registerImage(registry, SINGLE_READ_DERIVATE_MULTILINK,
"single_read_derivate_multilink-16x16-32.png");
+ registerImage(registry, CHARACTER_DATA_DERIVATE,
+ "character_data_derivate-16x16-32.png");
+
}
private void registerImage(ImageRegistry registry, String key,
import eu.etaxonomy.taxeditor.ui.combo.EnumComboElement;
import eu.etaxonomy.taxeditor.ui.combo.TermComboElement;
import eu.etaxonomy.taxeditor.ui.element.MinMaxTextSection.UnitType;
-import eu.etaxonomy.taxeditor.ui.mvc.OriginalLabelDataController;
-import eu.etaxonomy.taxeditor.ui.mvc.OriginalLabelDataElement;
import eu.etaxonomy.taxeditor.ui.openurl.IOpenUrlEnabled;
import eu.etaxonomy.taxeditor.ui.openurl.OpenUrlSelectorElement;
import eu.etaxonomy.taxeditor.ui.password.EditPasswordElement;
return element;
}
+ public OriginalLabelDataElement createOriginalLabelDataElement(ICdmFormElement parentElement) {
+ OriginalLabelDataElement element = new OriginalLabelDataElement(this, parentElement);
+ addAndAdaptElement(parentElement, element);
+ return element;
+ }
+
public PreservedSpecimenDetailElement createPreservedSpecimenDetailElement(ICdmFormElement parentElement) {
PreservedSpecimenDetailElement element = new PreservedSpecimenDetailElement(this, parentElement);
addAndAdaptElement(parentElement, element);
return section;
}
- /**
- * @param parentElement
- * @return
- */
- public OriginalLabelDataController createOriginalLabelDataController(AbstractCdmDetailSection<DerivedUnitFacade> parentElement) {
- OriginalLabelDataElement originalLabelDataElement = new OriginalLabelDataElement(parentElement.getLayoutComposite(), SWT.NONE);
- originalLabelDataElement.initController(this, parentElement);
- return originalLabelDataElement.getController();
- }
-
}
--- /dev/null
+// $Id$
+/**
+ * Copyright (C) 2014 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.taxeditor.ui.element;
+
+import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
+import eu.etaxonomy.taxeditor.ui.mvc.OriginalLabelDataField;
+import eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailElement;
+
+/**
+ * @author pplitzner
+ * @date 17.06.2014
+ *
+ */
+public class OriginalLabelDataElement extends AbstractCdmDetailElement<DerivedUnitFacade> {
+
+ private TextWithLabelElement textOriginalLabelData;
+
+ /**
+ * @param formFactory
+ * @param formElement
+ */
+ public OriginalLabelDataElement(CdmFormFactory formFactory,
+ ICdmFormElement formElement) {
+ super(formFactory, formElement);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#createControls
+ * (eu.etaxonomy.taxeditor.forms.ICdmFormElement, java.lang.Object, int)
+ */
+ @Override
+ protected void createControls(ICdmFormElement formElement,
+ DerivedUnitFacade entity, int style) {
+ new OriginalLabelDataField(formElement.getLayoutComposite(), style, entity.innerDerivedUnit(), getFormFactory());
+// textOriginalLabelData = formFactory.createTextWithLabelElement(formElement,
+// "Original Label Data", entity.innerDerivedUnit().getOriginalLabelInfo(), SWT.MULTI);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#handleEvent(java
+ * .lang.Object)
+ */
+ @Override
+ public void handleEvent(Object eventSource) {
+ if (eventSource == textOriginalLabelData) {
+ getEntity().innerDerivedUnit().setOriginalLabelInfo(textOriginalLabelData.getText());
+ }
+ }
+
+}
+++ /dev/null
-// $Id$
-/**
-* Copyright (C) 2014 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.taxeditor.ui.mvc;
-
-import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
-import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
-import eu.etaxonomy.taxeditor.ui.element.ICdmFormElement;
-import eu.etaxonomy.taxeditor.ui.mvc.interfaces.CdmCompositeController;
-import eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailElement;
-
-/**
- * @author pplitzner
- * @date 17.06.2014
- *
- */
-public class OriginalLabelDataController extends AbstractCdmDetailElement<DerivedUnitFacade> implements CdmCompositeController{
-
- private final OriginalLabelDataElement originalLabelDataElement;
-
- /**
- * @param dateTimeElement
- * @param formFactory
- * @param parentElement
- * @param initialDateTime
- * @param none
- */
- public OriginalLabelDataController(CdmFormFactory formFactory, ICdmFormElement parentElement, OriginalLabelDataElement originalLabelDataElement, int style) {
- super(formFactory, parentElement);
- this.originalLabelDataElement = originalLabelDataElement;
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.ui.element.IRelevantFormElement#setIrrelevant(boolean)
- */
- @Override
- public void setIrrelevant(boolean irrelevant) {
- // TODO Auto-generated method stub
-
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.ui.element.IEnableableFormElement#setEnabled(boolean)
- */
- @Override
- public void setEnabled(boolean enabled) {
- originalLabelDataElement.setEnabled(enabled);
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.ui.element.IEnableableFormElement#isEnabled()
- */
- @Override
- public boolean isEnabled() {
- return originalLabelDataElement.isEnabled();
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailElement#createControls(eu.etaxonomy.taxeditor.ui.element.ICdmFormElement, java.lang.Object, int)
- */
- @Override
- protected void createControls(ICdmFormElement formElement, DerivedUnitFacade entity, int style) {
- originalLabelDataElement.getText().setText(entity.getTitleCache());
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailElement#handleEvent(java.lang.Object)
- */
- @Override
- public void handleEvent(Object eventSource) {
- }
-}
+++ /dev/null
-// $Id$
-/**
-* Copyright (C) 2014 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.taxeditor.ui.mvc;
-
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.widgets.Composite;
-import org.eclipse.swt.widgets.Label;
-import org.eclipse.swt.widgets.Text;
-import org.eclipse.ui.forms.widgets.TableWrapData;
-import org.eclipse.ui.forms.widgets.TableWrapLayout;
-
-import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
-import eu.etaxonomy.taxeditor.ui.element.ICdmFormElement;
-
-/**
- * @author pplitzner
- * @date 17.06.2014
- *
- */
-public class OriginalLabelDataElement extends AbstractCdmComposite<OriginalLabelDataController>{
- private final Text text;
-
- /**
- * @param parent
- * @param style
- */
- public OriginalLabelDataElement(Composite parent, int style) {
- super(parent, style);
- {
- TableWrapLayout tableWrapLayout = new TableWrapLayout();
- tableWrapLayout.verticalSpacing = 0;
- tableWrapLayout.topMargin = 0;
- tableWrapLayout.rightMargin = 0;
- tableWrapLayout.leftMargin = 0;
- tableWrapLayout.horizontalSpacing = 0;
- tableWrapLayout.bottomMargin = 0;
- tableWrapLayout.numColumns = 3;
- setLayout(tableWrapLayout);
- }
-
- Label lblOriginalLabelData = new Label(this, SWT.NONE);
- lblOriginalLabelData.setLayoutData(new TableWrapData(TableWrapData.RIGHT, TableWrapData.TOP, 1, 1));
- lblOriginalLabelData.setText("Original Label Data");
-
- text = new Text(this, SWT.BORDER | SWT.READ_ONLY | SWT.WRAP | SWT.MULTI);
- text.setEditable(false);
- text.setLayoutData(new TableWrapData(TableWrapData.FILL_GRAB, TableWrapData.TOP, 1, 1));
- new Label(this, SWT.NONE);
-
- // TODO Auto-generated constructor stub
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.ui.mvc.AbstractCdmComposite#initInternalController(eu.etaxonomy.taxeditor.ui.element.CdmFormFactory, eu.etaxonomy.taxeditor.ui.element.ICdmFormElement)
- */
- @Override
- protected void initInternalController(CdmFormFactory formFactory, ICdmFormElement parentElement) {
- controller = new OriginalLabelDataController(formFactory, parentElement, this, SWT.NONE);
- }
-
- public Text getText() {
- return text;
- }
-}
--- /dev/null
+// $Id$
+/**
+* Copyright (C) 2014 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.taxeditor.ui.mvc;
+
+import java.util.List;
+
+import org.eclipse.core.databinding.DataBindingContext;
+import org.eclipse.core.databinding.beans.BeansObservables;
+import org.eclipse.core.databinding.observable.value.IObservableValue;
+import org.eclipse.jface.databinding.swt.SWTObservables;
+import org.eclipse.jface.util.IPropertyChangeListener;
+import org.eclipse.swt.SWT;
+import org.eclipse.swt.events.ModifyEvent;
+import org.eclipse.swt.events.ModifyListener;
+import org.eclipse.swt.layout.GridData;
+import org.eclipse.swt.layout.GridLayout;
+import org.eclipse.swt.widgets.Composite;
+import org.eclipse.swt.widgets.Label;
+import org.eclipse.swt.widgets.Text;
+
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
+import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
+import eu.etaxonomy.taxeditor.ui.element.CdmPropertyChangeEvent;
+
+/**
+ * @author pplitzner
+ * @date 23.06.2014
+ *
+ */
+public class OriginalLabelDataField extends Composite {
+
+ private DataBindingContext m_bindingContext;
+ private DerivedUnit derivedUnit = null;
+ private final Text originalLabelInfoText;
+ private CdmFormFactory formFactory;
+
+ public OriginalLabelDataField(Composite parent, int style, DerivedUnit newDerivedUnit, CdmFormFactory formFactory) {
+ this(parent, style);
+ setDerivedUnit(newDerivedUnit);
+ this.formFactory = formFactory;
+ }
+
+ public OriginalLabelDataField(Composite parent, int style) {
+ super(parent, style);
+ setLayout(new GridLayout(2, false));
+
+ new Label(this, SWT.NONE).setText("Original Label Data");
+
+ originalLabelInfoText = new Text(this, SWT.BORDER | SWT.WRAP | SWT.MULTI);
+ originalLabelInfoText.addModifyListener(new ModifyListener() {
+ @Override
+ public void modifyText(ModifyEvent e) {
+ if(formFactory!=null){
+ List<IPropertyChangeListener> propertyChangeListeners = formFactory.getPropertyChangeListeners();
+ for (IPropertyChangeListener iPropertyChangeListener : propertyChangeListeners) {
+ iPropertyChangeListener.propertyChange(new CdmPropertyChangeEvent(OriginalLabelDataField.this, e));
+ }
+ }
+ }
+ });
+ originalLabelInfoText.setLayoutData(new GridData(SWT.FILL, SWT.CENTER, true, false));
+
+ if (derivedUnit != null) {
+ m_bindingContext = initDataBindings();
+ }
+ }
+
+ @Override
+ protected void checkSubclass() {
+ // Disable the check that prevents subclassing of SWT components
+ }
+
+ private DataBindingContext initDataBindings() {
+ IObservableValue originalLabelInfoObserveWidget = SWTObservables.observeText(originalLabelInfoText, SWT.Modify);
+ IObservableValue originalLabelInfoObserveValue = BeansObservables
+ .observeValue(derivedUnit, "originalLabelInfo");
+ //
+ DataBindingContext bindingContext = new DataBindingContext();
+ //
+ bindingContext.bindValue(originalLabelInfoObserveWidget, originalLabelInfoObserveValue, null, null);
+ //
+ return bindingContext;
+ }
+
+ public DerivedUnit getDerivedUnit() {
+ return derivedUnit;
+ }
+
+ public void setDerivedUnit(DerivedUnit newDerivedUnit) {
+ setDerivedUnit(newDerivedUnit, true);
+ }
+
+ public void setDerivedUnit(DerivedUnit newDerivedUnit, boolean update) {
+ derivedUnit = newDerivedUnit;
+ if (update) {
+ if (m_bindingContext != null) {
+ m_bindingContext.dispose();
+ m_bindingContext = null;
+ }
+ if (derivedUnit != null) {
+ m_bindingContext = initDataBindings();
+ }
+ }
+ }
+
+}
import eu.etaxonomy.cdm.model.location.NamedArea;
import eu.etaxonomy.cdm.model.occurrence.Collection;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
+import eu.etaxonomy.taxeditor.preference.IPreferenceKeys;
+import eu.etaxonomy.taxeditor.preference.PreferencesUtil;
import eu.etaxonomy.taxeditor.ui.combo.EnumComboElement;
import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
import eu.etaxonomy.taxeditor.ui.element.GatheringEventUnitElement;
private TextWithLabelElement text_accessionNumber;
private GatheringEventUnitElement element_elevation;
-
+
/**
* @param formFactory
toggleableText_titleCache = formFactory.createToggleableTextField(
formElement, "Title Cache", entity.getTitleCache(),
entity.isProtectedTitleCache(), style);
- combo_specorobstype = formFactory
- .createEnumComboElement(SpecimenOrObservationType.class,
- formElement, style);
- combo_specorobstype.setSelection(entity.getType());
+
+ if(!PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.DETERMINATION_ONLY_FOR_FIELD_UNITS)){
+ combo_specorobstype = formFactory.createEnumComboElement(SpecimenOrObservationType.class, formElement,
+ style);
+ combo_specorobstype.setSelection(entity.getType());
+ }
selection_country = formFactory.createSelectionElement(NamedArea.class, getConversationHolder(),
formElement, "Country",
entity.getCountry(), EntitySelectionElement.NOTHING, style);
entity.getExactLocation(), style);
element_elevation = formFactory.createGatheringEventUnitElement(
formElement, "Elevation : ", entity, MinMaxTextSection.UnitType.ELEVATION, style);
-
+
element_date = formFactory.createTimePeriodElement(formElement, "Date",
entity.getGatheringPeriod(), style);
selection_collector = formFactory
import eu.etaxonomy.cdm.model.common.LanguageString;
import eu.etaxonomy.cdm.model.location.NamedArea;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
+import eu.etaxonomy.taxeditor.preference.IPreferenceKeys;
+import eu.etaxonomy.taxeditor.preference.PreferencesUtil;
import eu.etaxonomy.taxeditor.ui.combo.EnumComboElement;
import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
import eu.etaxonomy.taxeditor.ui.element.GatheringEventUnitElement;
protected void createControls(ICdmFormElement formElement, DerivedUnitFacade entity, int style) {
toggleableText_titleCache = formFactory.createToggleableTextField(formElement, "Title Cache",
entity.getTitleCache(), entity.isProtectedTitleCache(), style);
- combo_specorobstype = formFactory.createEnumComboElement(SpecimenOrObservationType.class, formElement, style);
- combo_specorobstype.setSelection(entity.getType());
+
+ if(!PreferencesUtil.getPreferenceStore().getBoolean(IPreferenceKeys.DETERMINATION_ONLY_FOR_FIELD_UNITS)){
+ combo_specorobstype = formFactory.createEnumComboElement(SpecimenOrObservationType.class, formElement, style);
+ combo_specorobstype.setSelection(entity.getType());
+ }
selection_country = formFactory.createSelectionElement(NamedArea.class, getConversationHolder(), formElement,
"Country", entity.getCountry(), EntitySelectionElement.NOTHING, style);
languageText_locality = formFactory.createLanguageStringWithLabelElement(formElement, "Locality",
element_point = formFactory.createPointElement(formElement, entity.getExactLocation(), style);
element_elevation = formFactory.createGatheringEventUnitElement(
formElement, "Elevation : ", entity, MinMaxTextSection.UnitType.ELEVATION, style);
-
+
element_date = formFactory.createTimePeriodElement(formElement, "Date", entity.getGatheringPeriod(), style);
selection_collector = formFactory.createSelectionElement(AgentBase.class, getConversationHolder(), formElement,
"Collector", entity.getCollector(), EntitySelectionElement.ALL, style);
*/
@Override
public String getHeading() {
- return "Original Label Data: ";
- }
-
- /* (non-Javadoc)
- * @see org.eclipse.ui.forms.widgets.ExpandableComposite#setText(java.lang.String)
- */
- @Override
- public void setText(String title) {
- String text = getHeading();
- if(getEntity()!=null){// && getEntity().getOriginalLabelData!=null){
- String titleCache = getEntity().getTitleCache();
- text += titleCache.substring(0, Math.min(10, titleCache.length()));
- text += "...";
- }
- if(text!=null){
- super.setText(text);
- }
- else{
- super.setText(title);
- }
+ return "Original Label Data";
}
/* (non-Javadoc)
*/
@Override
protected AbstractCdmDetailElement<DerivedUnitFacade> createCdmDetailElement(AbstractCdmDetailSection<DerivedUnitFacade> parentElement, int style) {
- return formFactory.createOriginalLabelDataController(parentElement);
+ return formFactory.createOriginalLabelDataElement(parentElement);
}
}
*/
package eu.etaxonomy.taxeditor.ui.section.occurrence.dna;
+import org.eclipse.swt.widgets.Text;
+
import eu.etaxonomy.cdm.model.common.DefinedTerm;
import eu.etaxonomy.cdm.model.common.TermType;
import eu.etaxonomy.cdm.model.molecular.Sequence;
private NumberWithLabelElement textConsensusSequenceLength;
private TextWithLabelElement textBarcodeSequence;
private TextWithLabelElement textGeneticAccessNo;
+ private UriWithLabelElement textNCBIUri;
+ private UriWithLabelElement textENAUri;
+ private UriWithLabelElement textDDBJUri;
private TextWithLabelElement textBoldProcessID;
private UriWithLabelElement textBoldUri;
@Override
protected void createControls(ICdmFormElement formElement, Sequence entity, int style) {
comboMarker = formFactory.createDefinedTermComboElement(TermType.DnaMarker, formElement, "DNA Marker", entity.getDnaMarker(), style);
- textConsensusSequence = formFactory.createTextWithLabelElement(formElement, "Consensus Sequence 5'->3'", entity.getConsensusSequence().getString(), style);
- textConsensusSequenceLength = formFactory.createNumberTextWithLabelElement(formElement, "Consensus Seq. Length", entity.getConsensusSequence().getLength(), style);
- textConsensusSequenceLength.setEnabled(false);
+// textConsensusSequence = formFactory.createTextWithLabelElement(formElement, "Consensus Sequence 5'->3'", entity.getConsensusSequence().getString(), style);
+// textConsensusSequenceLength = formFactory.createNumberTextWithLabelElement(formElement, "Consensus Seq. Length", entity.getConsensusSequence().getLength(), style);
+// ((Text) textConsensusSequenceLength.getMainControl()).setEditable(false);
textBarcodeSequence = formFactory.createTextWithLabelElement(formElement, "Barcode Sequence 5'->3'", entity.getBarcodeSequencePart()==null?"":entity.getBarcodeSequencePart().getString(), style);
textGeneticAccessNo = formFactory.createTextWithLabelElement(formElement, "Genetic Acc. No.", entity.getGeneticAccessionNumber(), style);
+ textNCBIUri = formFactory.createUriWithLabelElement(formElement, "NCBI URI", entity.getGenBankUri(), style);
+ ((Text) textNCBIUri.getMainControl()).setEditable(false);
+ textENAUri = formFactory.createUriWithLabelElement(formElement, "ENA URI", entity.getEmblUri(), style);
+ ((Text) textENAUri.getMainControl()).setEditable(false);
+ textDDBJUri = formFactory.createUriWithLabelElement(formElement, "DDBJ URI", entity.getDdbjUri(), style);
+ ((Text) textDDBJUri.getMainControl()).setEditable(false);
textBoldProcessID = formFactory.createTextWithLabelElement(formElement, "BOLD Process ID", entity.getBoldProcessId(), style);
textBoldUri = formFactory.createUriWithLabelElement(formElement, "BOLD URI", entity.getBoldUri(), style);
- textBoldUri.setEnabled(false);
-
+ ((Text) textBoldUri.getMainControl()).setEditable(false);
+ ((Text) textBoldUri.getMainControl()).setToolTipText("Query BOLD");
}
/*
getEntity().setConsensusSequence(consensusSequence);
textConsensusSequenceLength.setNumber(consensusSequence.getLength());
}
- else if(eventSource==textConsensusSequenceLength){
- // this is a derived value and should not be edited
- }
else if(eventSource==textBarcodeSequence){
SequenceString barcodeSequencePart = getEntity().getBarcodeSequencePart();
if(barcodeSequencePart==null){
}
else if(eventSource==textGeneticAccessNo){
getEntity().setGeneticAccessionNumber(textGeneticAccessNo.getText());
+ if(textGeneticAccessNo.getText()!=null && !textGeneticAccessNo.getText().isEmpty()){
+ textNCBIUri.setUri(getEntity().getGenBankUri());
+ textENAUri.setUri(getEntity().getEmblUri());
+ textDDBJUri.setUri(getEntity().getDdbjUri());
+ }
+ else{
+ textNCBIUri.setText("");
+ textENAUri.setText("");
+ textDDBJUri.setText("");
+ }
}
else if(eventSource==textBoldProcessID){
getEntity().setBoldProcessId(textBoldProcessID.getText());
textBoldUri.setText("");
}
}
- else if(eventSource==textBoldUri){
- //cannot be set because it is generated from the genetic access number and a base URI
- }
}
}
// $Id$
/**
* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
+* 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.
*/
import org.eclipse.ui.handlers.IHandlerService;
import org.eclipse.ui.part.ViewPart;
import org.eclipse.ui.progress.IWorkbenchSiteProgressService;
-import org.springframework.security.core.GrantedAuthority;
import eu.etaxonomy.cdm.config.ICdmSource;
-import eu.etaxonomy.cdm.database.ICdmDataSource;
import eu.etaxonomy.taxeditor.datasource.CdmDataSourceRepository;
+import eu.etaxonomy.taxeditor.model.AbstractUtility;
import eu.etaxonomy.taxeditor.model.ContextListenerAdapter;
import eu.etaxonomy.taxeditor.model.IContextListener;
import eu.etaxonomy.taxeditor.store.CdmStore;
-import eu.etaxonomy.taxeditor.store.StoreUtil;
/**
* <p>CdmDataSourceViewPart class.</p>
* @version 1.0
*/
public class CdmDataSourceViewPart extends ViewPart{
-
+
private static final Logger logger = Logger.getLogger(CdmDataSourceViewPart.class);
-
+
private class ContextListener extends ContextListenerAdapter{
/* (non-Javadoc)
* @see eu.etaxonomy.taxeditor.model.IContextListener#contextAboutToStop(org.eclipse.ui.IMemento, org.eclipse.core.runtime.IProgressMonitor)
@Override
public void contextAboutToStop(IMemento memento, IProgressMonitor monitor) {
monitor.subTask("Refreshing Datasource View");
- viewer.refresh();
+ viewer.refresh();
}
/* (non-Javadoc)
@Override
public void contextStop(IMemento memento, IProgressMonitor monitor) {
monitor.subTask("Refreshing Datasource View");
- viewer.refresh();
+ viewer.refresh();
}
/* (non-Javadoc)
viewer.refresh();
}
}
-
+
private class DataSourceJob extends Job{
- private List<ICdmSource> cdmSources;
+ private final List<ICdmSource> cdmSources;
/**
* @param name
public IStatus run(final IProgressMonitor monitor) {
try{
logger.debug("Begin of eclipse core runtime Job to Retrieve datasources");
- monitor.beginTask("Retrieving datasources", cdmSources.size() + 1);
-
+ monitor.beginTask("Retrieving datasources", cdmSources.size() + 1);
+
final List<CdmMetaDataAwareDataSourceContainer> containers = new ArrayList<CdmMetaDataAwareDataSourceContainer>();
-
+
for(ICdmSource cdmSource : cdmSources){
containers.add(new CdmMetaDataAwareDataSourceContainer(cdmSource));
}
-
+
Display.getDefault().asyncExec(new Runnable() {
-
+
@Override
public void run() {
viewer.setInput(containers);
}
});
monitor.worked(1);
-
+
for(final CdmMetaDataAwareDataSourceContainer container : containers){
-
-
- if(logger.isDebugEnabled()) logger.debug(" #" + container.hashCode() + " : next DataSourceContainer");
+
+
+ if(logger.isDebugEnabled()) {
+ logger.debug(" #" + container.hashCode() + " : next DataSourceContainer");
+ }
container.getMetaDataFromDataSource();
- if(logger.isDebugEnabled()) logger.debug(" #" + container.hashCode() + " : metadata retrieved, creating new runnable ...");
+ if(logger.isDebugEnabled()) {
+ logger.debug(" #" + container.hashCode() + " : metadata retrieved, creating new runnable ...");
+ }
Display.getDefault().asyncExec(new Runnable() {
-
+
@Override
public void run() {
- if(logger.isDebugEnabled()) logger.debug(" #" + container.hashCode() + " starting sub thread to update ...");
+ if(logger.isDebugEnabled()) {
+ logger.debug(" #" + container.hashCode() + " starting sub thread to update ...");
+ }
viewer.update(container, null);
- if(logger.isDebugEnabled()) logger.debug(" #" + container.hashCode() + " end of sub thread to update ...");
+ if(logger.isDebugEnabled()) {
+ logger.debug(" #" + container.hashCode() + " end of sub thread to update ...");
+ }
}
});
- if(logger.isDebugEnabled()) logger.debug(" #" + container.hashCode() + " done");
+ if(logger.isDebugEnabled()) {
+ logger.debug(" #" + container.hashCode() + " done");
+ }
monitor.worked(1);
}
-
+
}finally{
monitor.done();
}
return Status.OK_STATUS;
}
}
-
+
/** Constant <code>ID="eu.etaxonomy.taxeditor.store.datasource"{trunked}</code> */
public static String ID = "eu.etaxonomy.taxeditor.view.datasource";
-
+
private TableViewer viewer;
private String partNameCache;
private IWorkbenchSiteProgressService service;
-
+
private IContextListener contextListener;
private CdmDataSourceViewerComparator comparator;
-
+
/**
* <p>Constructor for CdmDataSourceViewPart.</p>
*/
public CdmDataSourceViewPart(){
}
-
+
/** {@inheritDoc} */
@Override
public void createPartControl(Composite parent) {
service = (IWorkbenchSiteProgressService) getSite().getAdapter(IWorkbenchSiteProgressService.class);
contextListener = new ContextListener();
CdmStore.getContextManager().addContextListener(contextListener);
-
+
// Create top composite
FillLayout fillLayout = new FillLayout();
fillLayout.marginWidth = 0;
fillLayout.marginHeight = 0;
- fillLayout.type = SWT.VERTICAL;
+ fillLayout.type = SWT.VERTICAL;
parent.setLayout(fillLayout);
-
+
viewer = new TableViewer(parent, SWT.MULTI | SWT.H_SCROLL
| SWT.V_SCROLL | SWT.FULL_SELECTION);
getSite().setSelectionProvider(viewer);
-
+
createColumns(viewer);
-
+
viewer.setContentProvider(new CdmDataSourceContentProvider());
viewer.setLabelProvider(new CdmDataSourceLabelProvider());
comparator = new CdmDataSourceViewerComparator();
viewer.setComparator(comparator);
-
-
+
+
// register context menu
MenuManager menuMgr = new MenuManager();
menuMgr.add(new GroupMarker(IWorkbenchActionConstants.MB_ADDITIONS));
Control control = viewer.getControl();
Menu menu = menuMgr.createContextMenu(control);
- control.setMenu(menu);
-
+ control.setMenu(menu);
+
// connect on doubleclick
viewer.addDoubleClickListener(new IDoubleClickListener() {
- public void doubleClick(DoubleClickEvent event) {
+ @Override
+ public void doubleClick(DoubleClickEvent event) {
if (event.getSelection() instanceof StructuredSelection) {
-
+
Object element = ((StructuredSelection) event
.getSelection()).getFirstElement();
if (element instanceof CdmMetaDataAwareDataSourceContainer) {
String commandId = "eu.etaxonomy.taxeditor.store.datasource.change";
-
+
ICommandService commandService = (ICommandService)getSite().getService(ICommandService.class);
-
- Command command = commandService.getCommand(commandId);
+
+ Command command = commandService.getCommand(commandId);
if(command.isEnabled()) {
-
- IHandlerService handlerService = (IHandlerService) StoreUtil.getService(IHandlerService.class);
-
+
+ IHandlerService handlerService = (IHandlerService) AbstractUtility.getService(IHandlerService.class);
+
try {
handlerService.executeCommand(commandId, null);
} catch (ExecutionException e) {
- StoreUtil.error(this.getClass(), e);
+ AbstractUtility.error(this.getClass(), e);
} catch (NotDefinedException e) {
- StoreUtil.error(this.getClass(), e);
+ AbstractUtility.error(this.getClass(), e);
} catch (NotEnabledException e) {
- StoreUtil.error(this.getClass(), e);
+ AbstractUtility.error(this.getClass(), e);
} catch (NotHandledException e) {
- StoreUtil.error(this.getClass(), e);
+ AbstractUtility.error(this.getClass(), e);
}
}
}
}
}
});
-
+
refresh();
}
-
+
// This will create the columns for the table
private void createColumns(TableViewer viewer) {
Table table = viewer.getTable();
table.setHeaderVisible(true);
table.setLinesVisible(true);
table.setSortDirection(SWT.UP);
-
+
}
-
+
/**
* <p>refresh</p>
*/
- public void refresh(){
+ public void refresh(){
getService().schedule(new DataSourceJob("Loading datasources", CdmDataSourceRepository.getAll()), Job.LONG);
}
/** {@inheritDoc} */
@Override
public void setFocus() {
- viewer.getControl().setFocus();
+// viewer.getControl().setFocus();
}
-
+
/* (non-Javadoc)
* @see org.eclipse.ui.part.WorkbenchPart#showBusy(boolean)
*/
public IWorkbenchSiteProgressService getService() {
return service;
}
-
+
private SelectionAdapter getSelectionAdapter(final TableColumn column,
final int index) {
SelectionAdapter selectionAdapter = new SelectionAdapter() {
import eu.etaxonomy.cdm.model.molecular.DnaSample;
import eu.etaxonomy.cdm.model.molecular.Sequence;
import eu.etaxonomy.cdm.model.molecular.SingleRead;
-import eu.etaxonomy.cdm.model.occurrence.Collection;
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
* @return
*/
public static String getDerivateText(Object element){
+ TreeNode parentNode = null;
if(element instanceof TreeNode){
+ parentNode = ((TreeNode) element).getParent();
//unwrap specimen from TreeNode
element = ((TreeNode) element).getValue();
}
label += mediaSpecimen.getMediaSpecimen().getTitle()!=null?mediaSpecimen.getMediaSpecimen().getTitle().getText()+", ":"[no motif]";
label += mediaSpecimen.getMediaSpecimen().getArtist()!=null?mediaSpecimen.getMediaSpecimen().getArtist()+", ":"";
label += mediaSpecimen.getAccessionNumber()!=null?mediaSpecimen.getAccessionNumber()+", ":"";
- Collection collection = mediaSpecimen.getCollection();
+ eu.etaxonomy.cdm.model.occurrence.Collection collection = mediaSpecimen.getCollection();
if(collection!=null){
label += collection.getName()!=null?collection.getName()+" ":"";
}
else if(element instanceof DnaSample
|| (element instanceof DerivedUnit
&& ((SpecimenOrObservationBase<?>) element).getRecordBasis()==SpecimenOrObservationType.DnaSample)){
- //TODO implement
- label += element.toString();
+ label += "SampleDesignation?";
}
else if(element instanceof DerivedUnit){
if(fieldUnits!=null && !fieldUnits.isEmpty()){
FieldUnit fieldUnit = fieldUnits.iterator().next();
GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
+// gatheringEvent = HibernateProxyHelper.deproxy(gatheringEvent, GatheringEvent.class);
if(gatheringEvent!=null){
label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+", ":"";
}
label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber()+", ":"";
}
- Collection collection = derivedUnit.getCollection();
+ eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
if(collection!=null){
label += collection.getName()!=null?collection.getName()+" ":"";
label += collection.getCode()!=null?"("+collection.getCode()+"), ":"";
}
else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
//TODO: implement
-// kindofTissue + SampleDesignation
+ label += "kindofTissue? + SampleDesignation?";
}
}
else if(element instanceof Sequence){
}
else if(element instanceof SingleRead){
SingleRead singleRead = (SingleRead)element;
+ label += "SampleDesignation?"+", ";
label += singleRead.getPrimer()!=null?singleRead.getPrimer().getLabel()+", ":"";
- label += "Marker?";
+ if(parentNode!=null && parentNode.getValue() instanceof Sequence){
+ Sequence sequence = (Sequence) parentNode.getValue();
+ label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():"";
+ }
}
else if(element instanceof SpecimenOrObservationBase){
SpecimenOrObservationBase<?> derivate = (SpecimenOrObservationBase<?>) element;
private final DerivateSearchComposite derivateSearchComposite;
private IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase<DerivedUnitFacadeCacheStrategy>> configurator;
private EnumTermComboController<SpecimenOrObservationType> enumTermComboController;
+ private final DerivateSearchView derivateSearchView;
/**
* @param parent
+ * @param derivateSearchView
*/
- public DerivateSearchCompositeController(Composite parent) {
+ public DerivateSearchCompositeController(Composite parent, DerivateSearchView derivateSearchView) {
this.derivateSearchComposite = new DerivateSearchComposite(parent, SWT.NONE);
+ this.derivateSearchView = derivateSearchView;
init();
}
}
private void searchDerivates(){
+ if(!derivateSearchView.getConversationHolder().isBound()){
+ derivateSearchView.setFocus(); //rebind the conversation
+ }
+
configurator.setTitleSearchString(derivateSearchComposite.getSearchField().getText());
SpecimenOrObservationType type = enumTermComboController.getSelection();
//filter by specimen type
public void reset(){
derivateSearchComposite.getResultViewer().setInput(null);
derivateSearchComposite.getSearchField().setText("");
+ enumTermComboController.setSelection(SpecimenOrObservationType.Unknown);
derivateSearchComposite.getComboDerivateType().deselectAll();
}
*/
@Override
public void createPartControl(Composite parent) {
- derivateSearchCompositeController = new DerivateSearchCompositeController(parent);
+ derivateSearchCompositeController = new DerivateSearchCompositeController(parent, this);
getSite().setSelectionProvider(derivateSearchCompositeController.getResultViewer());
derivateSearchCompositeController.setEnabled(CdmStore.isActive());
}
import org.eclipse.jface.util.IPropertyChangeListener;
import org.eclipse.jface.util.PropertyChangeEvent;
+import org.eclipse.swt.widgets.Control;
import org.eclipse.ui.forms.SectionPart;
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
if (event != null) {
Object eventSource = event.getSource();
+ Control[] children = formSection.getLayoutComposite().getChildren();
+ boolean containsElement = false;
+ for (Control control : children) {
+ if(eventSource.equals(control)){
+ containsElement = true;
+ break;
+ }
+ }
+ if(containsElement){
+ markDirty();
+ }
- if (formSection.equals(eventSource)){
+ else if (formSection.equals(eventSource)){
markDirty();
}
- if((
- (eventSource instanceof ICdmFormElement)
- && formSection.containsFormElement((ICdmFormElement) eventSource))
- ) {
- markDirty();
+ else if(((eventSource instanceof ICdmFormElement)&& formSection.containsFormElement((ICdmFormElement) eventSource))) {
+ markDirty();
}
}
}
<properties>
<java.codelevel>1.6</java.codelevel>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <cdmlib.version>3.3.7-SNAPSHOT</cdmlib.version>
+ <cdmlib.version>3.4.0-SNAPSHOT</cdmlib.version>
<!-- TODO can we use project.version ????? -->
<tycho.version>0.14.0</tycho.version>
<taxeditor.version>3.3.7-SNAPSHOT</taxeditor.version>
BGBM BDI Projects / taxeditor.git / commitdiff
