Revision 5ee7595c
ref #8679 move aggregation modes to own class file
| cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/DescriptionListController.java | ||
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| 39 | 39 |
import eu.etaxonomy.cdm.api.service.IDescriptionService; |
| 40 | 40 |
import eu.etaxonomy.cdm.api.service.ITermService; |
| 41 | 41 |
import eu.etaxonomy.cdm.api.service.IVocabularyService; |
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import eu.etaxonomy.cdm.api.service.description.DescriptionAggregationConfigurationBase.AggregationMode;
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import eu.etaxonomy.cdm.api.service.description.AggregationMode; |
|
| 43 | 43 |
import eu.etaxonomy.cdm.api.service.description.DistributionAggregation; |
| 44 | 44 |
import eu.etaxonomy.cdm.api.service.description.DistributionAggregationConfiguration; |
| 45 | 45 |
import eu.etaxonomy.cdm.api.service.dto.DistributionInfoDTO; |
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/description/AggregationMode.java | ||
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/** |
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* Copyright (C) 2019 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.cdm.api.service.description; |
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import java.util.Arrays; |
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import java.util.List; |
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public enum AggregationMode {
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WithinTaxon, |
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ToParent; |
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// public boolean isByRank() {
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// return this==byRanks || this == byAreasAndRanks; |
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// } |
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// public boolean isByArea() {
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// return this==byAreas || this == byAreasAndRanks; |
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// } |
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public static List<AggregationMode> byAreasAndRanks(){
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return Arrays.asList(new AggregationMode[]{AggregationMode.WithinTaxon, AggregationMode.ToParent});
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} |
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public static List<AggregationMode> byAreas(){
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return Arrays.asList(new AggregationMode[]{AggregationMode.WithinTaxon});
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} |
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public static List<AggregationMode> byRanks(){
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return Arrays.asList(new AggregationMode[]{AggregationMode.ToParent});
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} |
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} |
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| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/description/AggregationSourceMode.java | ||
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| 1 |
/** |
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* Copyright (C) 2019 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.cdm.api.service.description; |
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public enum AggregationSourceMode {
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NONE, |
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ALL, |
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ALL_SAMEVALUE, |
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DESCRIPTION, |
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TAXON; |
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} |
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| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/description/DescriptionAggregationBase.java | ||
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| 30 | 30 |
import eu.etaxonomy.cdm.api.service.ITaxonService; |
| 31 | 31 |
import eu.etaxonomy.cdm.api.service.ITermService; |
| 32 | 32 |
import eu.etaxonomy.cdm.api.service.UpdateResult; |
| 33 |
import eu.etaxonomy.cdm.api.service.description.DescriptionAggregationConfigurationBase.AggregationMode; |
|
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import eu.etaxonomy.cdm.common.DynamicBatch; |
| 35 | 34 |
import eu.etaxonomy.cdm.common.JvmLimitsException; |
| 36 | 35 |
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor; |
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/description/DescriptionAggregationConfigurationBase.java | ||
|---|---|---|
| 29 | 29 |
|
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private TaxonNodeFilter taxonNodeFilter; |
| 31 | 31 |
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private SourceMode toParentSourceMode = SourceMode.DESCRIPTION;
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private SourceMode withinTaxonSourceMode = SourceMode.ALL_SAMEVALUE;
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private AggregationSourceMode toParentSourceMode = AggregationSourceMode.DESCRIPTION;
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private AggregationSourceMode withinTaxonSourceMode = AggregationSourceMode.ALL_SAMEVALUE;
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|
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private List<AggregationMode> aggregationModes; |
| 36 | 36 |
|
| ... | ... | |
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private EnumSet<OriginalSourceType> aggregatingSourceTypes = EnumSet.of( |
| 47 | 47 |
OriginalSourceType.PrimaryTaxonomicSource, OriginalSourceType.PrimaryMediaSource); |
| 48 | 48 |
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// ************************** ENUMS ******************************/ |
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public enum AggregationMode {
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WithinTaxon, |
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ToParent; |
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// public boolean isByRank() {
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// return this==byRanks || this == byAreasAndRanks; |
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// } |
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// public boolean isByArea() {
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// return this==byAreas || this == byAreasAndRanks; |
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// } |
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public static List<AggregationMode> byAreasAndRanks(){
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return Arrays.asList(new AggregationMode[]{AggregationMode.WithinTaxon, AggregationMode.ToParent});
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} |
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public static List<AggregationMode> byAreas(){
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return Arrays.asList(new AggregationMode[]{AggregationMode.WithinTaxon});
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} |
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public static List<AggregationMode> byRanks(){
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return Arrays.asList(new AggregationMode[]{AggregationMode.ToParent});
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} |
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} |
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public enum SourceMode {
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NONE, |
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ALL, |
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ALL_SAMEVALUE, |
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DESCRIPTION, |
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TAXON; |
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} |
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//******************* CONSTRUCTOR **********************/ |
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|
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protected DescriptionAggregationConfigurationBase(TaxonNodeFilter filter, |
| ... | ... | |
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return this.aggregatingSourceTypes.remove(sourceTypeToRemove); |
| 138 | 107 |
} |
| 139 | 108 |
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public SourceMode getToParentSourceMode() {
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public AggregationSourceMode getToParentSourceMode() {
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return toParentSourceMode; |
| 142 | 111 |
} |
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public void setToParentSourceMode(SourceMode toParentSourceMode) {
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public void setToParentSourceMode(AggregationSourceMode toParentSourceMode) {
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this.toParentSourceMode = toParentSourceMode; |
| 145 | 114 |
} |
| 146 | 115 |
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public SourceMode getWithinTaxonSourceMode() {
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public AggregationSourceMode getWithinTaxonSourceMode() {
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return withinTaxonSourceMode; |
| 149 | 118 |
} |
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public void setWithinTaxonSourceMode(SourceMode withinTaxonSourceMode) {
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public void setWithinTaxonSourceMode(AggregationSourceMode withinTaxonSourceMode) {
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this.withinTaxonSourceMode = withinTaxonSourceMode; |
| 152 | 121 |
} |
| 153 | 122 |
public boolean isAdaptBatchSize() {
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| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/description/DistributionAggregation.java | ||
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| 23 | 23 |
import org.hibernate.search.Search; |
| 24 | 24 |
import org.springframework.transaction.TransactionStatus; |
| 25 | 25 |
|
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import eu.etaxonomy.cdm.api.service.description.DescriptionAggregationConfigurationBase.SourceMode; |
|
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import eu.etaxonomy.cdm.model.common.CdmBase; |
| 28 | 27 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| 29 | 28 |
import eu.etaxonomy.cdm.model.description.DescriptionElementSource; |
| ... | ... | |
| 181 | 180 |
* @param newStatus |
| 182 | 181 |
* @param additionalSourcesForWinningNewStatus Not in Use! |
| 183 | 182 |
* In the case when <code>newStatus</code> is preferred over <code>accumulatedStatus</code> these Set of sources will be added to the sources of <code>b</code> |
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* @param sourceMode
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* @param aggregationSourceMode
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* @return |
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*/ |
| 187 | 186 |
private StatusAndSources choosePreferredOrMerge(StatusAndSources accumulatedStatus, StatusAndSources newStatus, |
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Set<DescriptionElementSource> additionalSourcesForWinningNewStatus, SourceMode sourceMode){
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Set<DescriptionElementSource> additionalSourcesForWinningNewStatus, AggregationSourceMode aggregationSourceMode){
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| 189 | 188 |
|
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if (newStatus == null || newStatus.status == null) {
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return accumulatedStatus; |
| ... | ... | |
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if(additionalSourcesForWinningNewStatus != null) {
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newStatus.addSources(additionalSourcesForWinningNewStatus); |
| 211 | 210 |
} |
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if (sourceMode == SourceMode.ALL){
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if (aggregationSourceMode == AggregationSourceMode.ALL){
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newStatus.addSources(accumulatedStatus.sources); |
| 214 | 213 |
} |
| 215 | 214 |
return newStatus; |
| 216 | 215 |
} else {
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if (indexAcc == indexNew || sourceMode == SourceMode.ALL){
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if (indexAcc == indexNew || aggregationSourceMode == AggregationSourceMode.ALL){
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accumulatedStatus.addSources(newStatus.sources); |
| 219 | 218 |
} |
| 220 | 219 |
return accumulatedStatus; |
| ... | ... | |
| 310 | 309 |
|
| 311 | 310 |
// accumulate all sub area status |
| 312 | 311 |
StatusAndSources accumulatedStatusAndSources = null; |
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SourceMode sourceMode = getConfig().getWithinTaxonSourceMode();
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AggregationSourceMode aggregationSourceMode = getConfig().getWithinTaxonSourceMode();
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| 314 | 313 |
// TODO consider using the TermHierarchyLookup (only in local branch a.kohlbecker) |
| 315 | 314 |
Set<NamedArea> subAreas = getSubAreasFor(superArea); |
| 316 | 315 |
for(NamedArea subArea : subAreas){
|
| ... | ... | |
| 330 | 329 |
|| (getConfig().isIgnoreAbsentStatusByArea() && status.isAbsenceTerm())){
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continue; |
| 332 | 331 |
} |
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StatusAndSources subAreaStatusAndSources = new StatusAndSources(status, distribution, sourceMode);
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accumulatedStatusAndSources = choosePreferredOrMerge(accumulatedStatusAndSources, subAreaStatusAndSources, null, sourceMode);
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StatusAndSources subAreaStatusAndSources = new StatusAndSources(status, distribution, aggregationSourceMode);
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accumulatedStatusAndSources = choosePreferredOrMerge(accumulatedStatusAndSources, subAreaStatusAndSources, null, aggregationSourceMode);
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} |
| 336 | 335 |
} |
| 337 | 336 |
} // next sub area |
| 338 | 337 |
|
| 339 | 338 |
|
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if (accumulatedStatusAndSources != null) {
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StatusAndSources preferedStatus = choosePreferredOrMerge(accumulatedStatusMap.get(superArea), accumulatedStatusAndSources, null, sourceMode);
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StatusAndSources preferedStatus = choosePreferredOrMerge(accumulatedStatusMap.get(superArea), accumulatedStatusAndSources, null, aggregationSourceMode);
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accumulatedStatusMap.put(superArea, preferedStatus); |
| 343 | 342 |
} |
| 344 | 343 |
|
| ... | ... | |
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private final PresenceAbsenceTerm status; |
| 360 | 359 |
private final Set<DescriptionElementSource> sources = new HashSet<>(); |
| 361 | 360 |
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public StatusAndSources(PresenceAbsenceTerm status, DescriptionElementBase deb, SourceMode sourceMode) {
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public StatusAndSources(PresenceAbsenceTerm status, DescriptionElementBase deb, AggregationSourceMode aggregationSourceMode) {
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this.status = status; |
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if (sourceMode == SourceMode.NONE){
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if (aggregationSourceMode == AggregationSourceMode.NONE){
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return; |
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}else if (sourceMode == SourceMode.DESCRIPTION){
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}else if (aggregationSourceMode == AggregationSourceMode.DESCRIPTION){
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sources.add(DescriptionElementSource.NewAggregationInstance(deb.getInDescription())); |
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}else if (sourceMode == SourceMode.TAXON){
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}else if (aggregationSourceMode == AggregationSourceMode.TAXON){
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| 369 | 368 |
if (deb.getInDescription().isInstanceOf(TaxonDescription.class)){
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TaxonDescription td = CdmBase.deproxy(deb.getInDescription(), TaxonDescription.class); |
| 371 | 370 |
sources.add(DescriptionElementSource.NewAggregationInstance(td.getTaxon())); |
| 372 | 371 |
}else{
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logger.warn("Description is not of type TaxonDescription. Adding source not possible");
|
| 374 | 373 |
} |
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}else if (sourceMode == SourceMode.ALL || sourceMode == SourceMode.ALL_SAMEVALUE){
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}else if (aggregationSourceMode == AggregationSourceMode.ALL || aggregationSourceMode == AggregationSourceMode.ALL_SAMEVALUE){
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| 376 | 375 |
addSourcesDeduplicated(this.sources, deb.getSources()); |
| 377 | 376 |
}else{
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throw new RuntimeException("Unhandled source aggregation mode: " + sourceMode);
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throw new RuntimeException("Unhandled source aggregation mode: " + aggregationSourceMode);
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| 379 | 378 |
} |
| 380 | 379 |
} |
| 381 | 380 |
|
| ... | ... | |
| 430 | 429 |
} |
| 431 | 430 |
|
| 432 | 431 |
NamedArea area = distribution.getArea(); |
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SourceMode sourceMode = getConfig().getToParentSourceMode();
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AggregationSourceMode aggregationSourceMode = getConfig().getToParentSourceMode();
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| 434 | 433 |
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StatusAndSources childStatusAndSources = new StatusAndSources(status, distribution, sourceMode);
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StatusAndSources childStatusAndSources = new StatusAndSources(status, distribution, aggregationSourceMode);
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| 436 | 435 |
StatusAndSources preferedStatus = choosePreferredOrMerge(accumulatedStatusMap.get(area), |
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childStatusAndSources, null, sourceMode );
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childStatusAndSources, null, aggregationSourceMode );
|
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| 438 | 437 |
accumulatedStatusMap.put(area, preferedStatus); |
| 439 | 438 |
} |
| 440 | 439 |
|
| cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/description/DistributionAggregationTest.java | ||
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| 40 | 40 |
import eu.etaxonomy.cdm.api.service.IReferenceService; |
| 41 | 41 |
import eu.etaxonomy.cdm.api.service.ITaxonService; |
| 42 | 42 |
import eu.etaxonomy.cdm.api.service.ITermService; |
| 43 |
import eu.etaxonomy.cdm.api.service.description.DescriptionAggregationConfigurationBase.AggregationMode; |
|
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import eu.etaxonomy.cdm.api.service.description.DescriptionAggregationConfigurationBase.SourceMode; |
|
| 45 | 43 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 46 | 44 |
import eu.etaxonomy.cdm.common.JvmLimitsException; |
| 47 | 45 |
import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor; |
| ... | ... | |
| 310 | 308 |
TaxonNodeFilter filter = TaxonNodeFilter.NewInstance(null, null, null, null, null, lowerRank.getUuid(), upperRank.getUuid()); |
| 311 | 309 |
DistributionAggregationConfiguration config = DistributionAggregationConfiguration.NewInstance( |
| 312 | 310 |
AggregationMode.byAreasAndRanks(), superAreas, filter, monitor); |
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config.setToParentSourceMode(SourceMode.ALL_SAMEVALUE); |
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config.setToParentSourceMode(AggregationSourceMode.ALL_SAMEVALUE);
|
|
| 314 | 312 |
engine.invoke(config, repository); |
| 315 | 313 |
|
| 316 | 314 |
//test |
| ... | ... | |
| 463 | 461 |
TaxonNodeFilter filter = TaxonNodeFilter.NewInstance(null, null, null, null, null, lowerRank.getUuid(), upperRank.getUuid()); |
| 464 | 462 |
DistributionAggregationConfiguration config = DistributionAggregationConfiguration.NewInstance( |
| 465 | 463 |
AggregationMode.byAreasAndRanks(), superAreas, filter, monitor); |
| 466 |
config.setToParentSourceMode(SourceMode.ALL_SAMEVALUE); |
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config.setToParentSourceMode(AggregationSourceMode.ALL_SAMEVALUE);
|
|
| 467 | 465 |
engine.invoke(config, repository); |
| 468 | 466 |
|
| 469 | 467 |
Taxon lapsana_communis = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID); |
| ... | ... | |
| 518 | 516 |
TaxonNodeFilter filter = TaxonNodeFilter.NewInstance(null, null, null, null, null, lowerRank.getUuid(), upperRank.getUuid()); |
| 519 | 517 |
DistributionAggregationConfiguration config = DistributionAggregationConfiguration.NewInstance( |
| 520 | 518 |
AggregationMode.byAreasAndRanks(), superAreas, filter, monitor); |
| 521 |
config.setToParentSourceMode(SourceMode.ALL_SAMEVALUE); |
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config.setToParentSourceMode(AggregationSourceMode.ALL_SAMEVALUE);
|
|
| 522 | 520 |
engine.invoke(config, repository); |
| 523 | 521 |
|
| 524 | 522 |
Taxon lapsana_communis = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID); |
| ... | ... | |
| 598 | 596 |
} |
| 599 | 597 |
|
| 600 | 598 |
/** |
| 601 |
* Test to check if {@link SourceMode#DESCRIPTION} works for toParentAggregation.
|
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| 599 |
* Test to check if {@link AggregationSourceMode#DESCRIPTION} works for toParentAggregation.
|
|
| 602 | 600 |
*/ |
| 603 | 601 |
@Test |
| 604 | 602 |
@DataSets({
|
| ... | ... | |
| 621 | 619 |
TaxonNodeFilter filter = TaxonNodeFilter.NewInstance(null, null, null, null, null, lowerRank.getUuid(), upperRank.getUuid()); |
| 622 | 620 |
DistributionAggregationConfiguration config = DistributionAggregationConfiguration.NewInstance( |
| 623 | 621 |
AggregationMode.byRanks(), superAreas, filter, monitor); |
| 624 |
config.setToParentSourceMode(SourceMode.DESCRIPTION); |
|
| 622 |
config.setToParentSourceMode(AggregationSourceMode.DESCRIPTION);
|
|
| 625 | 623 |
engine.invoke(config, repository); |
| 626 | 624 |
|
| 627 | 625 |
Taxon lapsana_communis = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID); |
| ... | ... | |
| 636 | 634 |
} |
| 637 | 635 |
|
| 638 | 636 |
/** |
| 639 |
* Test to check if {@link SourceMode#DESCRIPTION} works for toParentAggregation.
|
|
| 637 |
* Test to check if {@link AggregationSourceMode#DESCRIPTION} works for toParentAggregation.
|
|
| 640 | 638 |
*/ |
| 641 | 639 |
@Test |
| 642 | 640 |
@DataSets({
|
| ... | ... | |
| 660 | 658 |
DistributionAggregationConfiguration config = DistributionAggregationConfiguration.NewInstance( |
| 661 | 659 |
AggregationMode.byAreasAndRanks(), superAreas, filter, monitor); |
| 662 | 660 |
config.setAggregatingSourceTypes(EnumSet.of(OriginalSourceType.PrimaryTaxonomicSource)); |
| 663 |
config.setToParentSourceMode(SourceMode.ALL); |
|
| 661 |
config.setToParentSourceMode(AggregationSourceMode.ALL);
|
|
| 664 | 662 |
engine.invoke(config, repository); |
| 665 | 663 |
|
| 666 | 664 |
//test |
| cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/description/StructuredDescriptionAggregationTest.java | ||
|---|---|---|
| 33 | 33 |
import eu.etaxonomy.cdm.api.service.ITermTreeService; |
| 34 | 34 |
import eu.etaxonomy.cdm.api.service.IVocabularyService; |
| 35 | 35 |
import eu.etaxonomy.cdm.api.service.UpdateResult; |
| 36 |
import eu.etaxonomy.cdm.api.service.description.DescriptionAggregationConfigurationBase.AggregationMode; |
|
| 37 | 36 |
import eu.etaxonomy.cdm.common.JvmLimitsException; |
| 38 | 37 |
import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor; |
| 39 | 38 |
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor; |
| cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/function/TestAggregations.java | ||
|---|---|---|
| 16 | 16 |
import org.apache.log4j.Logger; |
| 17 | 17 |
|
| 18 | 18 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
| 19 |
import eu.etaxonomy.cdm.api.service.description.DescriptionAggregationConfigurationBase.AggregationMode; |
|
| 20 |
import eu.etaxonomy.cdm.api.service.description.DescriptionAggregationConfigurationBase.SourceMode; |
|
| 21 | 19 |
import eu.etaxonomy.cdm.api.service.description.DistributionAggregationConfiguration; |
| 20 |
import eu.etaxonomy.cdm.api.service.description.AggregationMode; |
|
| 21 |
import eu.etaxonomy.cdm.api.service.description.AggregationSourceMode; |
|
| 22 | 22 |
import eu.etaxonomy.cdm.api.service.pager.Pager; |
| 23 | 23 |
import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor; |
| 24 | 24 |
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor; |
| ... | ... | |
| 127 | 127 |
List<UUID> areaList = areaPager.getRecords().stream().map(p ->p.getUuid()).collect(Collectors.toList()); |
| 128 | 128 |
DistributionAggregationConfiguration config = DistributionAggregationConfiguration |
| 129 | 129 |
.NewInstance(modes, areaList, filter, monitor); |
| 130 |
config.setToParentSourceMode(SourceMode.NONE); |
|
| 131 |
config.setWithinTaxonSourceMode(SourceMode.NONE); |
|
| 130 |
config.setToParentSourceMode(AggregationSourceMode.NONE);
|
|
| 131 |
config.setWithinTaxonSourceMode(AggregationSourceMode.NONE);
|
|
| 132 | 132 |
|
| 133 | 133 |
try {
|
| 134 | 134 |
config.getTaskInstance().invoke(config, appCtr); |
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