import java.util.ArrayList;
import java.util.Collection;
-import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import java.util.UUID;
import java.util.stream.Collectors;
import org.eclipse.swt.widgets.Button;
import org.eclipse.swt.widgets.Composite;
-import eu.etaxonomy.cdm.api.service.IDescriptionService;
import eu.etaxonomy.cdm.api.service.IDescriptiveDataSetService;
+import eu.etaxonomy.cdm.api.service.IPolytomousKeyService;
import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
import eu.etaxonomy.cdm.api.service.UpdateResult;
+import eu.etaxonomy.cdm.api.service.config.IdentifiableServiceConfiguratorImpl;
import eu.etaxonomy.cdm.api.service.dto.RowWrapperDTO;
+import eu.etaxonomy.cdm.api.service.dto.SpecimenRowWrapperDTO;
+import eu.etaxonomy.cdm.api.service.dto.TaxonRowWrapperDTO;
import eu.etaxonomy.cdm.common.CdmUtils;
import eu.etaxonomy.cdm.model.description.CategoricalData;
-import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
+import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
import eu.etaxonomy.cdm.model.description.Feature;
+import eu.etaxonomy.cdm.model.description.PolytomousKey;
import eu.etaxonomy.cdm.model.description.QuantitativeData;
import eu.etaxonomy.cdm.model.description.SpecimenDescription;
+import eu.etaxonomy.cdm.model.description.TaxonDescription;
import eu.etaxonomy.cdm.model.taxon.Taxon;
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
+import eu.etaxonomy.cdm.strategy.generate.PolytomousKeyGenerator;
+import eu.etaxonomy.cdm.strategy.generate.PolytomousKeyGeneratorConfigurator;
+import eu.etaxonomy.taxeditor.editor.l10n.Messages;
import eu.etaxonomy.taxeditor.model.ImageResources;
import eu.etaxonomy.taxeditor.model.MessagingUtils;
+import eu.etaxonomy.taxeditor.preference.IPreferenceKeys;
+import eu.etaxonomy.taxeditor.preference.PreferencesUtil;
import eu.etaxonomy.taxeditor.store.CdmStore;
+import eu.etaxonomy.taxeditor.store.StoreUtil;
import eu.etaxonomy.taxeditor.ui.dialog.selection.TaxonSelectionDialog;
/**
btnAddDescription.addSelectionListener(new SelectionAdapter() {
@Override
public void widgetSelected(SelectionEvent e) {
- String error = "";
+ if(StoreUtil.promptCheckIsDirty(matrix.getPart())){
+ return;
+ }
+ String error = ""; //$NON-NLS-1$
SpecimenSelectionDialog dialog = new SpecimenSelectionDialog(matrix.getShell(), matrix);
if(dialog.open()==Window.OK){
Collection<SpecimenNodeWrapper> wrappers = dialog.getSpecimen();
for (SpecimenNodeWrapper wrapper : wrappers) {
- SpecimenDescription description = CdmStore.getService(IDescriptiveDataSetService.class)
- .findDescriptionForDescriptiveDataSet(matrix.getDescriptiveDataSet().getUuid(),
- wrapper.getUuidAndTitleCache().getUuid());
- // description elements
- Map<Feature, DescriptionElementBase> featureToElementMap = new HashMap<>();
- Set<DescriptionElementBase> elements = description.getElements();
- for (DescriptionElementBase descriptionElementBase : elements) {
- Feature feature = descriptionElementBase.getFeature();
- featureToElementMap.put(feature, descriptionElementBase);
- }
- RowWrapperDTO rowWrapper = CdmStore.getService(IDescriptiveDataSetService.class).createRowWrapper(wrapper.getTaxonNode(), description, matrix.getDescriptiveDataSet());
+ SpecimenDescription specimenDescription = CdmStore.getService(IDescriptiveDataSetService.class)
+ .findSpecimenDescription(matrix.getDescriptiveDataSet().getUuid(),
+ wrapper.getUuidAndTitleCache().getUuid(), true);
+ SpecimenRowWrapperDTO rowWrapper = CdmStore.getService(IDescriptiveDataSetService.class)
+ .createSpecimenRowWrapper(specimenDescription, matrix.getDescriptiveDataSet());
if(rowWrapper==null){
- error += description;
+ error += specimenDescription;
continue;
}
+ //add specimen description
matrix.getDescriptions().add(rowWrapper);
- matrix.getDescriptiveDataSet().addDescription(description);
+ matrix.getDescriptiveDataSet().addDescription(specimenDescription);
+ matrix.getCdmEntitiySession().load(specimenDescription, true);
+
matrix.setDirty();
matrix.getSpecimenCache().remove(wrapper);
}
if(CdmUtils.isNotBlank(error)){
- MessagingUtils.warningDialog("Errors during row creation", this,
- String.format("Could not create rows for the following description:\n\n%s", error));
+ MessagingUtils.warningDialog(Messages.CharacterMatrixBottomToolbar_ERROR_ROW_CREATION_TITLE, this,
+ String.format(Messages.CharacterMatrixBottomToolbar_ERROR_ROW_CREATION_MESSAGE, error));
}
}
}
btnRemoveDescription.addSelectionListener(new SelectionAdapter() {
@Override
public void widgetSelected(SelectionEvent e) {
+ if(StoreUtil.promptCheckIsDirty(matrix.getPart())){
+ return;
+ }
+ if(!MessagingUtils.confirmDialog(Messages.CharacterMatrixBottomToolbar_CONFIRM_DELETE_TITLE, Messages.CharacterMatrixBottomToolbar_CONFIRM_DELETE_MESSAGE)){
+ return;
+ }
int[] fullySelectedRowPositions = matrix.getBodyLayer().getSelectionLayer().getFullySelectedRowPositions();
List<RowWrapperDTO> toRemove = new ArrayList<>();
for (int i : fullySelectedRowPositions) {
toRemove.add((RowWrapperDTO) rowObject);
}
}
- toRemove.forEach(rowToRemove->{
+ toRemove.forEach(rowToRemove -> {
matrix.getDescriptions().remove(rowToRemove);
- matrix.getDescriptiveDataSet().removeDescription(rowToRemove.getSpecimenDescription());
- matrix.setDirty();
+ CdmStore.getService(IDescriptiveDataSetService.class).removeDescription(
+ rowToRemove.getDescription().getUuid(), matrix.getDescriptiveDataSet().getUuid());
});
}
});
* Aggregate button
*/
Button btnAggregate = new Button(this, SWT.PUSH);
- btnAggregate.setText("Aggregate");
+ btnAggregate.setText(Messages.CharacterMatrixBottomToolbar_AGGREGATE);
btnAggregate.addSelectionListener(new SelectionAdapter() {
@Override
public void widgetSelected(SelectionEvent e) {
+ if(StoreUtil.promptCheckIsDirty(matrix.getPart())){
+ return;
+ }
List<TaxonNode> taxonSubtreeFilter = CdmStore.getService(IDescriptiveDataSetService.class).loadFilteredTaxonNodes(matrix.getDescriptiveDataSet(), null);
List<TaxonNodeDto> nodeDtos = taxonSubtreeFilter.stream()
.map(node -> new TaxonNodeDto(node)).collect(Collectors.toList());
TaxonNodeDto parentDto = CdmStore.getService(ITaxonNodeService.class).findCommonParentDto(nodeDtos);
UUID taxonUuid = parentDto.getTaxonUuid();
int response = MessagingUtils.confirmDialog(
- "Choose location for the aggregated description",
- String.format("The aggregated description will be stored at "
- + "the common parent taxon of this data set:\n%s\n\n"
- + "Do you want to use this taxon?"
- , parentDto.getTaxonTitleCache()), "Yes", "Choose taxon", "Cancel");
+ Messages.CharacterMatrixBottomToolbar_AGGREGATION_TITLE,
+ String.format(Messages.CharacterMatrixBottomToolbar_AGGREGATION_MESSAGE
+ , parentDto.getTaxonTitleCache()), Messages.CharacterMatrixBottomToolbar_YES, Messages.CharacterMatrixBottomToolbar_CHOOSE_TAXON, Messages.CharacterMatrixBottomToolbar_CANCEL);
if(response==2){
return;
}
}
List<UUID> descriptionUuids = new ArrayList<>();
matrix.getDescriptiveDataSet().getDescriptions().forEach(desc->descriptionUuids.add(desc.getUuid()));
- UpdateResult result = CdmStore.getService(IDescriptionService.class).aggregateDescription(taxonUuid, descriptionUuids, matrix.getDescriptiveDataSet().getLabel());
- matrix.addUpdateResult(result);
- matrix.setDirty();
+ UpdateResult result = CdmStore.getService(IDescriptiveDataSetService.class).aggregateDescription(taxonUuid, descriptionUuids, matrix.getDescriptiveDataSet().getLabel(), matrix.getDescriptiveDataSet().getUuid());
+ TaxonDescription taxonDescription = (TaxonDescription) result.getCdmEntity();
+ TaxonRowWrapperDTO taxonRowWrapper = CdmStore.getService(IDescriptiveDataSetService.class).createTaxonRowWrapper(taxonDescription.getUuid(), matrix.getDescriptiveDataSet().getUuid());
+ matrix.getDescriptions().add(taxonRowWrapper);
aggregateCategorcialHistogram(matrix.getFeatureToHistogramMap());
aggregateQuantitativeSummary(matrix.getFeatureToQuantDataStatisticsMap());
}
-
});
+ if(PreferencesUtil.getBooleanValue(IPreferenceKeys.SHOW_EXPERIMENTAL_FEATURES)){
+ /**
+ * Key generation button
+ */
+ Button btnGenerateKey = new Button(this, SWT.PUSH);
+ btnGenerateKey.setText("Generate Polytomous Key");
+ btnGenerateKey.addSelectionListener(new SelectionAdapter() {
+ @Override
+ public void widgetSelected(SelectionEvent e) {
+ if(StoreUtil.promptCheckIsDirty(matrix.getPart())){
+ return;
+ }
+ PolytomousKeyGeneratorConfigurator keyConfig = new PolytomousKeyGeneratorConfigurator();
+ DescriptiveDataSet descriptiveDataSet = matrix.getDescriptiveDataSet();
+ keyConfig.setDataSet(descriptiveDataSet);
+ PolytomousKey key = new PolytomousKeyGenerator().invoke(keyConfig);
+ IPolytomousKeyService keyService = CdmStore.getService(IPolytomousKeyService.class);
+ IdentifiableServiceConfiguratorImpl<PolytomousKey> serviceConfig= new IdentifiableServiceConfiguratorImpl<>();
+ serviceConfig.setTitleSearchString(descriptiveDataSet.getTitleCache());
+ List<PolytomousKey> list = keyService.findByTitle(serviceConfig).getRecords();
+ if(list!=null){
+ // TODO clear old key
+ System.out.println("Key with same name found for this data set found");
+ }
+ key.setTitleCache(descriptiveDataSet.getTitleCache(), true);
+ keyService.save(key);
+ key.print(System.out);
+ }
+ });
+ }
}
@SuppressWarnings("unchecked")
private void aggregateCategorcialHistogram(Map<Feature, CategoricalDataHistogram> featureToHistogramMap) {
featureToHistogramMap.clear();
- matrix.getDescriptions()
- .forEach(o -> ((RowWrapperDTO) o).getSpecimenDescription().getElements().stream()
- .filter(descriptionElement -> descriptionElement instanceof CategoricalData)
- .forEach(categoricalData -> {
- Feature feature = ((CategoricalData) categoricalData).getFeature();
- CategoricalDataHistogram dataHistogram = featureToHistogramMap.get(feature);
- if(dataHistogram==null){
- dataHistogram = new CategoricalDataHistogram(feature);
- }
- featureToHistogramMap.put(feature, dataHistogram);
- ((CategoricalData) categoricalData).getStateData()
- .forEach(stateData -> featureToHistogramMap.get(feature).addState(stateData.getState()));
- }));
+ matrix.getDescriptions().stream()
+ .filter(desc->desc instanceof SpecimenRowWrapperDTO)
+ .forEach(o -> ((SpecimenRowWrapperDTO) o).getDescription().getElements().stream()
+ .filter(descriptionElement -> descriptionElement instanceof CategoricalData)
+ .forEach(categoricalData -> {
+ Feature feature = ((CategoricalData) categoricalData).getFeature();
+ CategoricalDataHistogram dataHistogram = featureToHistogramMap.get(feature);
+ if(dataHistogram==null){
+ dataHistogram = new CategoricalDataHistogram(feature);
+ }
+ featureToHistogramMap.put(feature, dataHistogram);
+ ((CategoricalData) categoricalData).getStateData()
+ .forEach(stateData -> featureToHistogramMap.get(feature).addState(stateData.getState()));
+ }));
}
@SuppressWarnings("unchecked")
private void aggregateQuantitativeSummary(Map<Feature, QuantitativeDataStatistics> featureToQuantDataStatisticsMap) {
featureToQuantDataStatisticsMap.clear();
- matrix.getDescriptions()
- .forEach(o -> ((RowWrapperDTO) o).getSpecimenDescription().getElements().stream()
+ matrix.getDescriptions().stream()
+ .filter(desc->desc instanceof SpecimenRowWrapperDTO)
+ .forEach(o -> ((SpecimenRowWrapperDTO) o).getDescription().getElements().stream()
.filter(descriptionElement -> descriptionElement instanceof QuantitativeData)
.forEach(quantData -> {
Feature feature = ((QuantitativeData) quantData).getFeature();
BGBM BDI Projects / taxeditor.git / blobdiff