import java.util.ArrayList;
import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
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.IOccurrenceService;
+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.occurrence.SpecimenOrObservationBase;
+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.DescriptionHelper;
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) {
+ 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) {
- SpecimenOrObservationBase specimen = CdmStore.getService(IOccurrenceService.class).load(wrapper.getUuidAndTitleCache().getUuid());
- SpecimenDescription description = getDescriptionForDescriptiveDataSet(specimen);
- //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);
+ 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 += specimenDescription;
+ continue;
}
- RowWrapperDTO rowWrapper = CdmStore.getService(IDescriptiveDataSetService.class).createRowWrapper(description, matrix.getDescriptiveDataSet());
+ //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(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) {
- Set<TaxonNode> taxonSubtreeFilter = matrix.getDescriptiveDataSet().getTaxonSubtreeFilter();
+ 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;
}
}
taxonUuid = taxon.getUuid();
}
- UpdateResult result = CdmStore.getService(IDescriptionService.class).aggregateDescription(taxonUuid, null, matrix.getDescriptiveDataSet().getUuid());
- matrix.addUpdateResult(result);
- matrix.setDirty();
+ List<UUID> descriptionUuids = new ArrayList<>();
+ matrix.getDescriptiveDataSet().getDescriptions().forEach(desc->descriptionUuids.add(desc.getUuid()));
+ 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);
- //aggregate histogram for categorical tooltip
- Map<Feature, CategoricalDataHistogram> featureToHistogramMap = matrix.getFeatureToHistogramMap();
- featureToHistogramMap.clear();
- aggregateCategorcialHistogram(featureToHistogramMap);
+ 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) {
- 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()));
- }));
+ featureToHistogramMap.clear();
+ 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()));
+ }));
}
- private SpecimenDescription getDescriptionForDescriptiveDataSet(SpecimenOrObservationBase specimen){
- Set<Feature> wsFeatures = matrix.getDescriptiveDataSet().getDescriptiveSystem().getDistinctFeatures();
- List<DescriptionElementBase> matchingDescriptionElements = new ArrayList<>();
-
- for (SpecimenDescription specimenDescription : (Set<SpecimenDescription>) specimen.getDescriptions()) {
- specimenDescription = (SpecimenDescription) CdmStore.getService(IDescriptionService.class).load(specimenDescription.getUuid());
- Set<Feature> specimenDescriptionFeatures = new HashSet<>();
- //gather specimen description features and check for match with WS features
- for (DescriptionElementBase specimenDescriptionElement : specimenDescription.getElements()) {
- Feature feature = specimenDescriptionElement.getFeature();
- specimenDescriptionFeatures.add(feature);
- if(wsFeatures.contains(feature)){
- matchingDescriptionElements.add(specimenDescriptionElement);
- }
- }
- //if description with the exact same features is found return the description
- if(specimenDescriptionFeatures.equals(wsFeatures)){
- return specimenDescription;
- }
- }
- //Create new specimen description if no match was found
- matrix.setDirty();
- SpecimenDescription newDesription = SpecimenDescription.NewInstance(specimen);
- newDesription.setTitleCache(Messages.CharacterMatrix_DESCRIPTIVE_DATA_SET+matrix.getDescriptiveDataSet().getLabel()+": "+newDesription.generateTitle(), true); //$NON-NLS-2$
-
- //check for equals description element (same feature and same values)
- Map<Feature, List<DescriptionElementBase>> featureToElementMap = new HashMap<>();
- for(DescriptionElementBase element:matchingDescriptionElements){
- List<DescriptionElementBase> list = featureToElementMap.get(element.getFeature());
- if(list==null){
- list = new ArrayList<>();
- }
- list.add(element);
- featureToElementMap.put(element.getFeature(), list);
- }
- Set<DescriptionElementBase> descriptionElementsToClone = new HashSet<>();
- for(Feature feature:featureToElementMap.keySet()){
- List<DescriptionElementBase> elements = featureToElementMap.get(feature);
- //no duplicate description elements found for this feature
- if(elements.size()==1){
- descriptionElementsToClone.add(elements.get(0));
- }
- //duplicates found -> check if all are equal
- else{
- DescriptionElementBase match = null;
- for (DescriptionElementBase descriptionElementBase : elements) {
- if(match==null){
- match = descriptionElementBase;
- }
- else if(!new DescriptionElementCompareWrapper(match).equals(new DescriptionElementCompareWrapper(descriptionElementBase))){
- match = null;
- MessagingUtils.informationDialog(Messages.CharacterMatrix_MULTIPLE_DATA,
- String.format(Messages.CharacterMatrix_MULTIPLE_DATA_MESSAGE, feature.getLabel()));
- break;
+ @SuppressWarnings("unchecked")
+ private void aggregateQuantitativeSummary(Map<Feature, QuantitativeDataStatistics> featureToQuantDataStatisticsMap) {
+ featureToQuantDataStatisticsMap.clear();
+ 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();
+ QuantitativeDataStatistics dataStatistics = featureToQuantDataStatisticsMap.get(feature);
+ if(dataStatistics==null){
+ dataStatistics = new QuantitativeDataStatistics();
}
- }
- if(match!=null){
- descriptionElementsToClone.add(match);
- }
- }
- }
- //clone matching descriptionElements
- for (DescriptionElementBase descriptionElementBase : descriptionElementsToClone) {
- DescriptionElementBase clone;
- try {
- clone = descriptionElementBase.clone(newDesription);
- clone.getSources().forEach(source -> source.setOriginalNameString(DescriptionHelper.getLabel(descriptionElementBase)));
- } catch (CloneNotSupportedException e) {
- MessagingUtils.error(CharacterMatrix.class, e);
- }
- }
-
- //add all remaining description elements to the new description
- for(Feature wsFeature:wsFeatures){
- boolean featureFound = false;
- for(DescriptionElementBase element:newDesription.getElements()){
- if(element.getFeature().equals(wsFeature)){
- featureFound = true;
- break;
- }
- }
- if(!featureFound){
- if(wsFeature.isSupportsCategoricalData()){
- newDesription.addElement(CategoricalData.NewInstance(wsFeature));
- }
- else if(wsFeature.isSupportsQuantitativeData()){
- newDesription.addElement(QuantitativeData.NewInstance(wsFeature));
- }
- }
- }
- return newDesription;
-
+ featureToQuantDataStatisticsMap.put(feature, dataStatistics);
+ dataStatistics.addQuantitativeData((QuantitativeData) quantData);
+ }));
}
+
}
BGBM BDI Projects / taxeditor.git / blobdiff