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Merge branch 'main' into feature/2312-external-recommender-v2
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* main: (68 commits)
  #4316 - Dissolve generic API module
  #4316 - Dissolve generic API module
  #4316 - Dissolve generic API module
  #4316 - Dissolve generic API module
  #4316 - Dissolve generic API module
  #4316 - Dissolve generic API module
  #4314 - Move project API to own module
  #4308 - Support for custom XML formats
  #4308 - Support for custom XML formats
  #4308 - Support for custom XML formats
  #4310 - Viewport tracking does not work well in RecogitoJS editor
  #4308 - Support for custom XML formats
  #4302 - Files imported as HTML do not show properly in HTML-based editor
  #4305 - New predictions message is shown even if no new predictions were generated
  #4304 - Log more startup messages through boot logger
  #4229 - Better project template selection
  #4298 - Recommender status says "Waiting for evaluation" for recommenders that cannot be evaluated
  #4297 - Popover always showing "tag not in tagset" even if feature has no tagset at all
  #4294 - Infer paragraph boundaries when displaying plain text files in HTML-based editors
  #4150 - Upgrade dependencies
  ...
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reckart committed Nov 21, 2023
2 parents 527ac03 + b7d928f commit d8b115f
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2 changes: 1 addition & 1 deletion inception/inception-active-learning/pom.xml
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Expand Up @@ -44,7 +44,7 @@
</dependency>
<dependency>
<groupId>de.tudarmstadt.ukp.inception.app</groupId>
<artifactId>inception-api-schema</artifactId>
<artifactId>inception-schema-api</artifactId>
</dependency>
<dependency>
<groupId>de.tudarmstadt.ukp.inception.app</groupId>
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Expand Up @@ -29,7 +29,7 @@
import de.tudarmstadt.ukp.inception.recommendation.api.model.SpanSuggestion;
import de.tudarmstadt.ukp.inception.recommendation.api.model.SuggestionGroup;
import de.tudarmstadt.ukp.inception.recommendation.api.model.SuggestionGroup.Delta;
import de.tudarmstadt.ukp.inception.schema.adapter.AnnotationException;
import de.tudarmstadt.ukp.inception.schema.api.adapter.AnnotationException;

public interface ActiveLearningService
{
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Expand Up @@ -52,9 +52,9 @@
import de.tudarmstadt.ukp.inception.recommendation.api.model.SpanSuggestion;
import de.tudarmstadt.ukp.inception.recommendation.api.model.SuggestionGroup;
import de.tudarmstadt.ukp.inception.recommendation.api.model.SuggestionGroup.Delta;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.adapter.AnnotationException;
import de.tudarmstadt.ukp.inception.schema.feature.FeatureSupportRegistry;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.adapter.AnnotationException;
import de.tudarmstadt.ukp.inception.schema.api.feature.FeatureSupportRegistry;

/**
* <p>
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Expand Up @@ -34,8 +34,8 @@
import de.tudarmstadt.ukp.inception.recommendation.api.LearningRecordService;
import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService;
import de.tudarmstadt.ukp.inception.recommendation.config.RecommenderServiceAutoConfiguration;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.feature.FeatureSupportRegistry;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.feature.FeatureSupportRegistry;

@Configuration
@AutoConfigureAfter(RecommenderServiceAutoConfiguration.class)
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Expand Up @@ -122,11 +122,11 @@
import de.tudarmstadt.ukp.inception.rendering.vmodel.VMarker;
import de.tudarmstadt.ukp.inception.rendering.vmodel.VRange;
import de.tudarmstadt.ukp.inception.rendering.vmodel.VTextMarker;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.adapter.AnnotationException;
import de.tudarmstadt.ukp.inception.schema.feature.FeatureEditor;
import de.tudarmstadt.ukp.inception.schema.feature.FeatureSupport;
import de.tudarmstadt.ukp.inception.schema.feature.FeatureSupportRegistry;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.adapter.AnnotationException;
import de.tudarmstadt.ukp.inception.schema.api.feature.FeatureEditor;
import de.tudarmstadt.ukp.inception.schema.api.feature.FeatureSupport;
import de.tudarmstadt.ukp.inception.schema.api.feature.FeatureSupportRegistry;

public class ActiveLearningSidebar
extends AnnotationSidebar_ImplBase
Expand Down Expand Up @@ -1103,8 +1103,8 @@ public void onSpanCreated(SpanCreatedEvent aEvent)
return;
}

reactToAnnotationsBeingCreatedOrDeleted(aEvent.getRequestTarget(), aEvent.getLayer(),
aEvent.getDocument());
reactToAnnotationsBeingCreatedOrDeleted(aEvent.getRequestTarget().orElse(null),
aEvent.getLayer(), aEvent.getDocument());
}

@OnEvent
Expand All @@ -1122,7 +1122,7 @@ public void onRelationCreated(RelationCreatedEvent aEvent)
return;
}

reactToAnnotationsBeingCreatedOrDeleted(aEvent.getRequestTarget(), aEvent.getLayer(),
reactToAnnotationsBeingCreatedOrDeleted(aEvent.getRequestTarget().get(), aEvent.getLayer(),
aEvent.getDocument());
}

Expand Down Expand Up @@ -1153,7 +1153,7 @@ public void onFeatureValueUpdated(FeatureValueUpdatedEvent aEvent)
return;
}

reactToAnnotationsBeingCreatedOrDeleted(aEvent.getRequestTarget(),
reactToAnnotationsBeingCreatedOrDeleted(aEvent.getRequestTarget().get(),
aEvent.getFeature().getLayer(), aEvent.getDocument());
}

Expand All @@ -1180,7 +1180,7 @@ public void onAnnotationDeleted(SpanDeletedEvent aEvent)
return;
}

reactToAnnotationsBeingCreatedOrDeleted(aEvent.getRequestTarget(), aEvent.getLayer(),
reactToAnnotationsBeingCreatedOrDeleted(aEvent.getRequestTarget().get(), aEvent.getLayer(),
aEvent.getDocument());
}

Expand Down Expand Up @@ -1381,7 +1381,7 @@ public void onDocumentOpenedEvent(DocumentOpenedEvent aEvent)
// If active learning is not active, update the sidebar in case the session auto-terminated
ActiveLearningUserState alState = alStateModel.getObject();
if (!alState.isSessionActive()) {
aEvent.getRequestTarget().add(alMainContainer);
aEvent.getRequestTarget().ifPresent(target -> target.add(alMainContainer));
return;
}

Expand All @@ -1390,11 +1390,11 @@ public void onDocumentOpenedEvent(DocumentOpenedEvent aEvent)

// Maybe the prediction switch has made a new suggestion available for us to go to
if (alState.getSuggestion().isEmpty()) {
moveToNextSuggestion(aEvent.getRequestTarget());
moveToNextSuggestion(aEvent.getRequestTarget().get());
return;
}

refreshCurrentSuggestionOrMoveToNextSuggestion(aEvent.getRequestTarget());
refreshCurrentSuggestionOrMoveToNextSuggestion(aEvent.getRequestTarget().get());
}

@OnEvent
Expand All @@ -1405,7 +1405,7 @@ public void onPredictionsSwitched(PredictionsSwitchedEvent aEvent)
// If active learning is not active, update the sidebar in case the session auto-terminated
ActiveLearningUserState alState = alStateModel.getObject();
if (!alState.isSessionActive()) {
aEvent.getRequestTarget().add(alMainContainer);
aEvent.getRequestTarget().ifPresent(target -> target.add(alMainContainer));
return;
}

Expand All @@ -1414,11 +1414,11 @@ public void onPredictionsSwitched(PredictionsSwitchedEvent aEvent)

// Maybe the prediction switch has made a new suggestion available for us to go to
if (alState.getSuggestion().isEmpty()) {
moveToNextSuggestion(aEvent.getRequestTarget());
moveToNextSuggestion(aEvent.getRequestTarget().get());
return;
}

refreshCurrentSuggestionOrMoveToNextSuggestion(aEvent.getRequestTarget());
refreshCurrentSuggestionOrMoveToNextSuggestion(aEvent.getRequestTarget().get());
}

private void refreshCurrentSuggestionOrMoveToNextSuggestion(AjaxRequestTarget aTarget)
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Expand Up @@ -103,12 +103,12 @@ private IconType getStateIcon()
@OnEvent
public void sessionStarted(ActiveLearningSessionStartedEvent aEvent)
{
aEvent.getRequestTarget().add(this);
aEvent.getRequestTarget().ifPresent(target -> target.add(this));
}

@OnEvent
public void sessionStarted(ActiveLearningSessionCompletedEvent aEvent)
{
aEvent.getRequestTarget().add(this);
aEvent.getRequestTarget().ifPresent(target -> target.add(this));
}
}
4 changes: 2 additions & 2 deletions inception/inception-agreement/pom.xml
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Expand Up @@ -62,11 +62,11 @@
</dependency>
<dependency>
<groupId>de.tudarmstadt.ukp.inception.app</groupId>
<artifactId>inception-api</artifactId>
<artifactId>inception-project-api</artifactId>
</dependency>
<dependency>
<groupId>de.tudarmstadt.ukp.inception.app</groupId>
<artifactId>inception-api-schema</artifactId>
<artifactId>inception-schema-api</artifactId>
</dependency>
<dependency>
<groupId>de.tudarmstadt.ukp.inception.app</groupId>
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Expand Up @@ -39,7 +39,7 @@
import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.api.DiffAdapter;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
import de.tudarmstadt.ukp.clarin.webanno.model.Tag;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;

public class CohenKappaAgreementMeasure
extends CodingAgreementMeasure_ImplBase<DefaultAgreementTraits>
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Expand Up @@ -25,7 +25,7 @@
import de.tudarmstadt.ukp.clarin.webanno.agreement.results.coding.AbstractCodingAgreementMeasureSupport;
import de.tudarmstadt.ukp.clarin.webanno.agreement.results.coding.CodingAgreementResult;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;

@Component
public class CohenKappaAgreementMeasureSupport
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Expand Up @@ -39,7 +39,7 @@
import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.api.DiffAdapter;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
import de.tudarmstadt.ukp.clarin.webanno.model.Tag;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;

public class FleissKappaAgreementMeasure
extends CodingAgreementMeasure_ImplBase<DefaultAgreementTraits>
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Expand Up @@ -25,7 +25,7 @@
import de.tudarmstadt.ukp.clarin.webanno.agreement.results.coding.AbstractCodingAgreementMeasureSupport;
import de.tudarmstadt.ukp.clarin.webanno.agreement.results.coding.CodingAgreementResult;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;

@Component
public class FleissKappaAgreementMeasureSupport
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Expand Up @@ -41,7 +41,7 @@
import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.api.DiffAdapter;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
import de.tudarmstadt.ukp.clarin.webanno.model.Tag;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;

public class KrippendorffAlphaAgreementMeasure
extends CodingAgreementMeasure_ImplBase<KrippendorffAlphaAgreementTraits>
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Expand Up @@ -26,7 +26,7 @@
import de.tudarmstadt.ukp.clarin.webanno.agreement.results.coding.AbstractCodingAgreementMeasureSupport;
import de.tudarmstadt.ukp.clarin.webanno.agreement.results.coding.CodingAgreementResult;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;

@Component
public class KrippendorffAlphaAgreementMeasureSupport
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Expand Up @@ -38,7 +38,7 @@
import de.tudarmstadt.ukp.clarin.webanno.agreement.measures.AgreementMeasure_ImplBase;
import de.tudarmstadt.ukp.clarin.webanno.agreement.results.unitizing.UnitizingAgreementResult;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;

public class KrippendorffAlphaUnitizingAgreementMeasure
extends AgreementMeasure_ImplBase<//
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Expand Up @@ -36,7 +36,7 @@
import de.tudarmstadt.ukp.clarin.webanno.agreement.results.unitizing.UnitizingAgreementResult;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;

@Component
public class KrippendorffAlphaUnitizingAgreementMeasureSupport
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Expand Up @@ -71,7 +71,6 @@
import de.tudarmstadt.ukp.clarin.webanno.agreement.AgreementUtils;
import de.tudarmstadt.ukp.clarin.webanno.agreement.PairwiseAnnotationResult;
import de.tudarmstadt.ukp.clarin.webanno.agreement.measures.DefaultAgreementTraits;
import de.tudarmstadt.ukp.clarin.webanno.api.ProjectService;
import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff;
import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.api.DiffAdapter;
import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
Expand All @@ -84,7 +83,8 @@
import de.tudarmstadt.ukp.clarin.webanno.support.wicket.AjaxDownloadBehavior;
import de.tudarmstadt.ukp.clarin.webanno.support.wicket.AjaxDownloadLink;
import de.tudarmstadt.ukp.inception.documents.api.DocumentService;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.project.api.ProjectService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;

public class PairwiseCodingAgreementTable
extends Panel
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Expand Up @@ -43,13 +43,13 @@
import de.agilecoders.wicket.core.markup.html.bootstrap.components.TooltipConfig.Placement;
import de.tudarmstadt.ukp.clarin.webanno.agreement.AgreementResult;
import de.tudarmstadt.ukp.clarin.webanno.agreement.PairwiseAnnotationResult;
import de.tudarmstadt.ukp.clarin.webanno.api.ProjectService;
import de.tudarmstadt.ukp.clarin.webanno.security.UserDao;
import de.tudarmstadt.ukp.clarin.webanno.support.DefaultRefreshingView;
import de.tudarmstadt.ukp.clarin.webanno.support.DescriptionTooltipBehavior;
import de.tudarmstadt.ukp.clarin.webanno.support.bootstrap.PopoverBehavior;
import de.tudarmstadt.ukp.inception.documents.api.DocumentService;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.project.api.ProjectService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;

public class PairwiseUnitizingAgreementTable
extends Panel
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Expand Up @@ -70,7 +70,7 @@
import de.tudarmstadt.ukp.inception.annotation.layer.chain.ChainLayerSupport;
import de.tudarmstadt.ukp.inception.annotation.layer.relation.RelationLayerSupport;
import de.tudarmstadt.ukp.inception.annotation.layer.span.SpanLayerSupport;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.service.FeatureSupportRegistryImpl;

@ExtendWith(MockitoExtension.class)
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4 changes: 2 additions & 2 deletions inception/inception-annotation-storage/pom.xml
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Expand Up @@ -52,7 +52,7 @@
</dependency>
<dependency>
<groupId>de.tudarmstadt.ukp.inception.app</groupId>
<artifactId>inception-api</artifactId>
<artifactId>inception-project-api</artifactId>
</dependency>
<dependency>
<groupId>de.tudarmstadt.ukp.inception.app</groupId>
Expand All @@ -68,7 +68,7 @@
</dependency>
<dependency>
<groupId>de.tudarmstadt.ukp.inception.app</groupId>
<artifactId>inception-api-schema</artifactId>
<artifactId>inception-schema-api</artifactId>
</dependency>
<dependency>
<groupId>de.tudarmstadt.ukp.inception.app</groupId>
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Expand Up @@ -17,7 +17,6 @@
*/
package de.tudarmstadt.ukp.inception.annotation.storage;

import static de.tudarmstadt.ukp.clarin.webanno.api.ProjectService.withProjectLogger;
import static de.tudarmstadt.ukp.clarin.webanno.api.annotation.util.WebAnnoCasUtil.getRealCas;
import static de.tudarmstadt.ukp.clarin.webanno.api.annotation.util.WebAnnoCasUtil.transferCasOwnershipToCurrentThread;
import static de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasAccessMode.EXCLUSIVE_WRITE_ACCESS;
Expand All @@ -27,6 +26,7 @@
import static de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasUpgradeMode.AUTO_CAS_UPGRADE;
import static de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasUpgradeMode.NO_CAS_UPGRADE;
import static de.tudarmstadt.ukp.inception.annotation.storage.CasStorageServiceImpl.RepairAndUpgradeFlags.ISOLATED_SESSION;
import static de.tudarmstadt.ukp.inception.project.api.ProjectService.withProjectLogger;
import static java.lang.System.currentTimeMillis;
import static java.util.Collections.newSetFromMap;
import static java.util.Collections.synchronizedSet;
Expand Down Expand Up @@ -75,7 +75,6 @@
import de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasStorageServiceLoader;
import de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasUpgradeMode;
import de.tudarmstadt.ukp.clarin.webanno.api.casstorage.ConcurentCasModificationException;
import de.tudarmstadt.ukp.clarin.webanno.api.event.LayerConfigurationChangedEvent;
import de.tudarmstadt.ukp.clarin.webanno.diag.CasDoctor;
import de.tudarmstadt.ukp.clarin.webanno.diag.CasDoctorException;
import de.tudarmstadt.ukp.clarin.webanno.model.Project;
Expand All @@ -84,7 +83,8 @@
import de.tudarmstadt.ukp.inception.annotation.storage.config.CasStorageCacheProperties;
import de.tudarmstadt.ukp.inception.annotation.storage.config.CasStorageServiceAutoConfiguration;
import de.tudarmstadt.ukp.inception.annotation.storage.driver.CasStorageDriver;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.event.LayerConfigurationChangedEvent;

/**
* <p>
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Expand Up @@ -29,7 +29,7 @@
import de.tudarmstadt.ukp.inception.annotation.storage.driver.CasStorageDriver;
import de.tudarmstadt.ukp.inception.annotation.storage.driver.filesystem.FileSystemCasStorageDriver;
import de.tudarmstadt.ukp.inception.documents.api.RepositoryProperties;
import de.tudarmstadt.ukp.inception.schema.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;

@Configuration
@EnableConfigurationProperties({ CasStorageCachePropertiesImpl.class,
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Expand Up @@ -17,11 +17,11 @@
*/
package de.tudarmstadt.ukp.inception.annotation.storage.driver.filesystem;

import static de.tudarmstadt.ukp.clarin.webanno.api.ProjectService.ANNOTATION_FOLDER;
import static de.tudarmstadt.ukp.clarin.webanno.api.ProjectService.DOCUMENT_FOLDER;
import static de.tudarmstadt.ukp.clarin.webanno.api.ProjectService.PROJECT_FOLDER;
import static de.tudarmstadt.ukp.clarin.webanno.api.annotation.util.WebAnnoCasUtil.setDocumentId;
import static de.tudarmstadt.ukp.clarin.webanno.support.logging.BaseLoggers.BOOT_LOG;
import static de.tudarmstadt.ukp.inception.project.api.ProjectService.ANNOTATION_FOLDER;
import static de.tudarmstadt.ukp.inception.project.api.ProjectService.DOCUMENT_FOLDER;
import static de.tudarmstadt.ukp.inception.project.api.ProjectService.PROJECT_FOLDER;
import static java.lang.System.currentTimeMillis;
import static java.nio.file.Files.move;
import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;
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Expand Up @@ -62,7 +62,6 @@
import de.tudarmstadt.ukp.clarin.webanno.api.annotation.util.WebAnnoCasUtil;
import de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasProvider;
import de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasSessionException;
import de.tudarmstadt.ukp.clarin.webanno.api.event.LayerConfigurationChangedEvent;
import de.tudarmstadt.ukp.clarin.webanno.api.type.CASMetadata;
import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
Expand All @@ -72,6 +71,7 @@
import de.tudarmstadt.ukp.inception.annotation.storage.config.CasStoragePropertiesImpl;
import de.tudarmstadt.ukp.inception.annotation.storage.driver.filesystem.FileSystemCasStorageDriver;
import de.tudarmstadt.ukp.inception.documents.api.RepositoryProperties;
import de.tudarmstadt.ukp.inception.schema.api.event.LayerConfigurationChangedEvent;

public class CasStorageServiceImplTest
{
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