| 12 |
12 |
import java.util.Collection;
|
| 13 |
13 |
import java.util.List;
|
| 14 |
14 |
import java.util.Map;
|
| 15 |
|
import java.util.Optional;
|
| 16 |
15 |
import java.util.UUID;
|
| 17 |
16 |
|
| 18 |
17 |
import org.eclipse.core.runtime.ICoreRunnable;
|
| ... | ... | |
| 34 |
33 |
|
| 35 |
34 |
import eu.etaxonomy.cdm.api.application.CdmApplicationState;
|
| 36 |
35 |
import eu.etaxonomy.cdm.api.service.IDescriptiveDataSetService;
|
| 37 |
|
import eu.etaxonomy.cdm.api.service.IOccurrenceService;
|
| 38 |
36 |
import eu.etaxonomy.cdm.api.service.IPolytomousKeyService;
|
| 39 |
|
import eu.etaxonomy.cdm.api.service.ITaxonService;
|
| 40 |
37 |
import eu.etaxonomy.cdm.api.service.UpdateResult;
|
| 41 |
38 |
import eu.etaxonomy.cdm.api.service.config.DescriptionAggregationConfiguration;
|
| 42 |
39 |
import eu.etaxonomy.cdm.api.service.config.IdentifiableServiceConfiguratorImpl;
|
| ... | ... | |
| 45 |
42 |
import eu.etaxonomy.cdm.common.CdmUtils;
|
| 46 |
43 |
import eu.etaxonomy.cdm.common.monitor.IRemotingProgressMonitor;
|
| 47 |
44 |
import eu.etaxonomy.cdm.model.description.CategoricalData;
|
| 48 |
|
import eu.etaxonomy.cdm.model.description.DescriptionType;
|
| 49 |
45 |
import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
|
| 50 |
46 |
import eu.etaxonomy.cdm.model.description.Feature;
|
| 51 |
|
import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
|
| 52 |
47 |
import eu.etaxonomy.cdm.model.description.PolytomousKey;
|
| 53 |
48 |
import eu.etaxonomy.cdm.model.description.QuantitativeData;
|
| 54 |
|
import eu.etaxonomy.cdm.model.description.SpecimenDescription;
|
| 55 |
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
| 56 |
|
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
|
| 57 |
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
| 58 |
49 |
import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
|
| 59 |
50 |
import eu.etaxonomy.cdm.strategy.generate.PolytomousKeyGenerator;
|
| 60 |
51 |
import eu.etaxonomy.cdm.strategy.generate.PolytomousKeyGeneratorConfigurator;
|
| ... | ... | |
| 99 |
90 |
if(StoreUtil.promptCheckIsDirty(matrix.getPart())){
|
| 100 |
91 |
return;
|
| 101 |
92 |
}
|
| 102 |
|
String error = ""; //$NON-NLS-1$
|
| 103 |
93 |
SpecimenSelectionDialog dialog = new SpecimenSelectionDialog(matrix.getShell(), matrix);
|
| 104 |
94 |
if(dialog.open()==Window.OK){
|
| 105 |
95 |
Collection<SpecimenNodeWrapper> wrappers = dialog.getSpecimen();
|
| 106 |
|
if(wrappers.stream().anyMatch(wrapper->wrapper.getTaxonDescription()==null)
|
|
96 |
if(wrappers.stream().anyMatch(wrapper->wrapper.getTaxonDescriptionUuid()==null)
|
| 107 |
97 |
&& !MessagingUtils.confirmDialog(
|
| 108 |
98 |
"Create Taxon Association",
|
| 109 |
99 |
"Some specimens are not linked with taxon via IndividualsAssociation yet.\n"
|
| 110 |
100 |
+ "Do you want to create this association?")){
|
| 111 |
101 |
return;
|
| 112 |
102 |
}
|
|
103 |
String error = ""; //$NON-NLS-1$
|
| 113 |
104 |
for (SpecimenNodeWrapper wrapper : wrappers) {
|
| 114 |
|
TaxonDescription taxonDescription = wrapper.getTaxonDescription();
|
| 115 |
|
if(taxonDescription==null){
|
| 116 |
|
Optional<TaxonDescription> associationDescriptionOptional = wrapper.getTaxonNode().getTaxon().getDescriptions().stream()
|
| 117 |
|
.filter(desc->desc.getTypes().contains(DescriptionType.INDIVIDUALS_ASSOCIATION))
|
| 118 |
|
.findFirst();
|
| 119 |
|
Taxon taxon = wrapper.getTaxonNode().getTaxon();
|
| 120 |
|
if(!associationDescriptionOptional.isPresent()){
|
| 121 |
|
taxonDescription = TaxonDescription.NewInstance(taxon);
|
| 122 |
|
}
|
| 123 |
|
else{
|
| 124 |
|
taxonDescription = associationDescriptionOptional.get();
|
| 125 |
|
}
|
| 126 |
|
|
| 127 |
|
SpecimenOrObservationBase specimen = CdmStore.getService(IOccurrenceService.class).load(wrapper.getUuidAndTitleCache().getUuid());
|
| 128 |
|
IndividualsAssociation association = IndividualsAssociation.NewInstance(specimen);
|
| 129 |
|
taxonDescription.addElement(association);
|
| 130 |
|
CdmStore.getService(ITaxonService.class).saveOrUpdate(wrapper.getTaxonNode().getTaxon());
|
| 131 |
|
}
|
| 132 |
|
SpecimenDescription specimenDescription = CdmStore.getService(IDescriptiveDataSetService.class)
|
| 133 |
|
.findSpecimenDescription(matrix.getDescriptiveDataSet().getUuid(),
|
| 134 |
|
wrapper.getUuidAndTitleCache().getUuid(), true);
|
| 135 |
105 |
SpecimenRowWrapperDTO rowWrapper = CdmStore.getService(IDescriptiveDataSetService.class)
|
| 136 |
|
.createSpecimenRowWrapper(specimenDescription, matrix.getDescriptiveDataSet());
|
|
106 |
.addRowWrapperToDataset(wrapper, matrix.getDescriptiveDataSet().getUuid());
|
| 137 |
107 |
if(rowWrapper==null){
|
| 138 |
|
error += specimenDescription+"\n";
|
|
108 |
error += wrapper.getUuidAndTitleCache().getTitleCache();
|
|
109 |
error += "\n";
|
| 139 |
110 |
continue;
|
| 140 |
111 |
}
|
|
112 |
|
| 141 |
113 |
//add wrapper to matrix
|
| 142 |
114 |
matrix.getDescriptions().add(rowWrapper);
|
| 143 |
|
//add specimen description to data set
|
| 144 |
|
matrix.getDescriptiveDataSet().addDescription(specimenDescription);
|
| 145 |
|
//add taxon description with IndividualsAssociation to the specimen to data set
|
| 146 |
|
matrix.getDescriptiveDataSet().addDescription(taxonDescription);
|
| 147 |
|
matrix.getCdmEntitiySession().load(specimenDescription, true);
|
| 148 |
|
matrix.getCdmEntitiySession().load(taxonDescription, true);
|
|
115 |
// matrix.getCdmEntitiySession().load(specimenDescription, true);
|
|
116 |
// matrix.getCdmEntitiySession().load(taxonDescription, true);
|
| 149 |
117 |
|
| 150 |
118 |
matrix.setDirty();
|
| 151 |
119 |
matrix.getSpecimenCache().remove(wrapper);
|
ref #8539 Performance and session handling fixes