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Merge pull request #4322 from inception-project/refactoring/4321-Orga…
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…nize-packages

#4321 - Organize packages
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reckart authored Nov 24, 2023
2 parents de89391 + 4467de5 commit 37c01ef
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5 changes: 4 additions & 1 deletion inception/inception-active-learning/pom.xml
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<groupId>de.tudarmstadt.ukp.inception.app</groupId>
<artifactId>inception-support</artifactId>
</dependency>

<dependency>
<groupId>de.tudarmstadt.ukp.inception.app</groupId>
<artifactId>inception-support-bootstrap</artifactId>
</dependency>
<dependency>
<groupId>de.tudarmstadt.ukp.inception.app</groupId>
<artifactId>inception-recommendation</artifactId>
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import org.springframework.context.ApplicationEvent;

import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.support.wicket.event.HybridApplicationUIEvent;
import de.tudarmstadt.ukp.inception.support.wicket.event.HybridApplicationUIEvent;

public class ActiveLearningSessionCompletedEvent
extends ApplicationEvent
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import org.springframework.context.ApplicationEvent;

import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.support.wicket.event.HybridApplicationUIEvent;
import de.tudarmstadt.ukp.inception.support.wicket.event.HybridApplicationUIEvent;

public class ActiveLearningSessionStartedEvent
extends ApplicationEvent
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import java.util.List;
import java.util.stream.Collectors;

import de.tudarmstadt.ukp.clarin.webanno.support.JSONUtil;
import de.tudarmstadt.ukp.inception.active.learning.config.ActiveLearningAutoConfiguration;
import de.tudarmstadt.ukp.inception.active.learning.event.ActiveLearningRecommendationEvent;
import de.tudarmstadt.ukp.inception.log.adapter.EventLoggingAdapter;
import de.tudarmstadt.ukp.inception.log.model.AnnotationDetails;
import de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordType;
import de.tudarmstadt.ukp.inception.support.json.JSONUtil;

/**
* <p>
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import java.util.List;
import java.util.stream.Collectors;

import de.tudarmstadt.ukp.clarin.webanno.support.JSONUtil;
import de.tudarmstadt.ukp.inception.active.learning.config.ActiveLearningAutoConfiguration;
import de.tudarmstadt.ukp.inception.active.learning.event.ActiveLearningRecommendationEvent;
import de.tudarmstadt.ukp.inception.active.learning.event.ActiveLearningSuggestionOfferedEvent;
import de.tudarmstadt.ukp.inception.log.adapter.EventLoggingAdapter;
import de.tudarmstadt.ukp.inception.log.model.AnnotationDetails;
import de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordType;
import de.tudarmstadt.ukp.inception.support.json.JSONUtil;

/**
* <p>
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import static de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasAccessMode.SHARED_READ_ONLY_ACCESS;
import static de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasUpgradeMode.AUTO_CAS_UPGRADE;
import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.SPAN_TYPE;
import static de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaBehavior.visibleWhen;
import static de.tudarmstadt.ukp.inception.active.learning.sidebar.ActiveLearningUserStateMetaData.CURRENT_AL_USER_STATE;
import static de.tudarmstadt.ukp.inception.recommendation.api.model.AnnotationSuggestion.FLAG_REJECTED;
import static de.tudarmstadt.ukp.inception.recommendation.api.model.AnnotationSuggestion.FLAG_SKIPPED;
import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordType.ACCEPTED;
import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordType.CORRECTED;
import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordType.REJECTED;
import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.SPAN_TYPE;
import static de.tudarmstadt.ukp.inception.support.lambda.LambdaBehavior.visibleWhen;
import static java.lang.String.format;
import static java.util.Arrays.asList;
import static java.util.stream.Collectors.toList;
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import de.tudarmstadt.ukp.clarin.webanno.model.ReorderableTag;
import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
import de.tudarmstadt.ukp.clarin.webanno.security.UserDao;
import de.tudarmstadt.ukp.clarin.webanno.support.bootstrap.BootstrapModalDialog;
import de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaAjaxButton;
import de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaAjaxLink;
import de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaAjaxSubmitLink;
import de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaBehavior;
import de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaChoiceRenderer;
import de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaModelAdapter;
import de.tudarmstadt.ukp.clarin.webanno.support.spring.ApplicationEventPublisherHolder;
import de.tudarmstadt.ukp.clarin.webanno.support.uima.ICasUtil;
import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.AnnotationPage;
import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.sidebar.AnnotationSidebar_ImplBase;
import de.tudarmstadt.ukp.inception.active.learning.ActiveLearningService;
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import de.tudarmstadt.ukp.inception.annotation.layer.relation.RelationCreatedEvent;
import de.tudarmstadt.ukp.inception.annotation.layer.span.SpanCreatedEvent;
import de.tudarmstadt.ukp.inception.annotation.layer.span.SpanDeletedEvent;
import de.tudarmstadt.ukp.inception.bootstrap.BootstrapModalDialog;
import de.tudarmstadt.ukp.inception.documents.api.DocumentService;
import de.tudarmstadt.ukp.inception.editor.action.AnnotationActionHandler;
import de.tudarmstadt.ukp.inception.recommendation.api.LearningRecordService;
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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;
import de.tudarmstadt.ukp.inception.support.lambda.LambdaAjaxButton;
import de.tudarmstadt.ukp.inception.support.lambda.LambdaAjaxLink;
import de.tudarmstadt.ukp.inception.support.lambda.LambdaAjaxSubmitLink;
import de.tudarmstadt.ukp.inception.support.lambda.LambdaBehavior;
import de.tudarmstadt.ukp.inception.support.lambda.LambdaChoiceRenderer;
import de.tudarmstadt.ukp.inception.support.lambda.LambdaModelAdapter;
import de.tudarmstadt.ukp.inception.support.spring.ApplicationEventPublisherHolder;
import de.tudarmstadt.ukp.inception.support.uima.ICasUtil;

public class ActiveLearningSidebar
extends AnnotationSidebar_ImplBase
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*/
package de.tudarmstadt.ukp.inception.active.learning.sidebar;

import de.tudarmstadt.ukp.clarin.webanno.support.dialog.ConfirmationDialogContentPanel_ImplBase;
import de.tudarmstadt.ukp.inception.bootstrap.dialog.ConfirmationDialogContentPanel_ImplBase;

public class HistoryItemDeleteConfirmationDialogPanel
extends ConfirmationDialogContentPanel_ImplBase
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4 changes: 4 additions & 0 deletions inception/inception-agreement/pom.xml
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<groupId>de.tudarmstadt.ukp.inception.app</groupId>
<artifactId>inception-api-annotation</artifactId>
</dependency>
<dependency>
<groupId>de.tudarmstadt.ukp.inception.app</groupId>
<artifactId>inception-support-bootstrap</artifactId>
</dependency>

<dependency>
<groupId>org.dkpro.statistics</groupId>
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import org.springframework.stereotype.Component;

import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
import de.tudarmstadt.ukp.clarin.webanno.support.logging.BaseLoggers;
import de.tudarmstadt.ukp.inception.support.logging.BaseLoggers;

@Component
public class AgreementMeasureSupportRegistryImpl
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*/
package de.tudarmstadt.ukp.clarin.webanno.agreement.measures;

import static de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaBehavior.visibleWhen;
import static de.tudarmstadt.ukp.inception.support.lambda.LambdaBehavior.visibleWhen;
import static java.util.Arrays.asList;

import org.apache.wicket.markup.html.form.CheckBox;
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*/
package de.tudarmstadt.ukp.clarin.webanno.agreement.measures.krippendorffalphaunitizing;

import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.SPAN_TYPE;
import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.SPAN_TYPE;

import java.util.List;
import java.util.Map;
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import static de.tudarmstadt.ukp.clarin.webanno.model.AnchoringMode.SINGLE_TOKEN;
import static de.tudarmstadt.ukp.clarin.webanno.model.AnchoringMode.TOKENS;
import static de.tudarmstadt.ukp.clarin.webanno.model.LinkMode.NONE;
import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.RELATION_TYPE;
import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.SPAN_TYPE;
import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.RELATION_TYPE;
import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.SPAN_TYPE;
import static java.util.Arrays.asList;

import java.util.List;
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import static de.tudarmstadt.ukp.clarin.webanno.agreement.AgreementReportExportFormat.CSV;
import static de.tudarmstadt.ukp.clarin.webanno.agreement.AgreementUtils.makeCodingStudy;
import static de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff.doDiff;
import static de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaBehavior.enabledWhen;
import static de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaBehavior.visibleWhen;
import static de.tudarmstadt.ukp.inception.support.lambda.LambdaBehavior.enabledWhen;
import static de.tudarmstadt.ukp.inception.support.lambda.LambdaBehavior.visibleWhen;
import static java.util.Arrays.asList;
import static java.util.stream.Collectors.toCollection;

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import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
import de.tudarmstadt.ukp.clarin.webanno.model.Tag;
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.clarin.webanno.support.lambda.LambdaAjaxFormComponentUpdatingBehavior;
import de.tudarmstadt.ukp.clarin.webanno.support.wicket.AjaxDownloadBehavior;
import de.tudarmstadt.ukp.clarin.webanno.support.wicket.AjaxDownloadLink;
import de.tudarmstadt.ukp.inception.bootstrap.PopoverBehavior;
import de.tudarmstadt.ukp.inception.documents.api.DocumentService;
import de.tudarmstadt.ukp.inception.project.api.ProjectService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.support.lambda.LambdaAjaxFormComponentUpdatingBehavior;
import de.tudarmstadt.ukp.inception.support.wicket.AjaxDownloadBehavior;
import de.tudarmstadt.ukp.inception.support.wicket.AjaxDownloadLink;
import de.tudarmstadt.ukp.inception.support.wicket.DefaultRefreshingView;
import de.tudarmstadt.ukp.inception.support.wicket.DescriptionTooltipBehavior;

public class PairwiseCodingAgreementTable
extends Panel
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*/
package de.tudarmstadt.ukp.clarin.webanno.agreement.results.unitizing;

import static de.tudarmstadt.ukp.clarin.webanno.support.lambda.LambdaBehavior.visibleWhen;
import static de.tudarmstadt.ukp.inception.support.lambda.LambdaBehavior.visibleWhen;

import java.util.ArrayList;
import java.util.List;
Expand All @@ -44,12 +44,12 @@
import de.tudarmstadt.ukp.clarin.webanno.agreement.AgreementResult;
import de.tudarmstadt.ukp.clarin.webanno.agreement.PairwiseAnnotationResult;
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.bootstrap.PopoverBehavior;
import de.tudarmstadt.ukp.inception.documents.api.DocumentService;
import de.tudarmstadt.ukp.inception.project.api.ProjectService;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.support.wicket.DefaultRefreshingView;
import de.tudarmstadt.ukp.inception.support.wicket.DescriptionTooltipBehavior;

public class PairwiseUnitizingAgreementTable
extends Panel
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import static de.tudarmstadt.ukp.clarin.webanno.model.LinkMode.WITH_ROLE;
import static de.tudarmstadt.ukp.clarin.webanno.model.MultiValueMode.ARRAY;
import static de.tudarmstadt.ukp.clarin.webanno.model.OverlapMode.NO_OVERLAP;
import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.SPAN_TYPE;
import static de.tudarmstadt.ukp.clarin.webanno.support.uima.AnnotationBuilder.buildAnnotation;
import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.SPAN_TYPE;
import static de.tudarmstadt.ukp.inception.support.uima.AnnotationBuilder.buildAnnotation;
import static java.util.Arrays.asList;
import static org.apache.uima.cas.CAS.TYPE_NAME_STRING;
import static org.apache.uima.fit.factory.CasFactory.createCas;
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import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.model.TagSet;
import de.tudarmstadt.ukp.clarin.webanno.support.uima.AnnotationBuilder;
import de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS;
import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Lemma;
import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token;
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import de.tudarmstadt.ukp.inception.annotation.layer.span.SpanLayerSupport;
import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.service.FeatureSupportRegistryImpl;
import de.tudarmstadt.ukp.inception.support.uima.AnnotationBuilder;

@ExtendWith(MockitoExtension.class)
public class AgreementMeasureTestSuite_ImplBase
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import static de.tudarmstadt.ukp.clarin.webanno.agreement.AgreementUtils.dumpAgreementStudy;
import static de.tudarmstadt.ukp.clarin.webanno.agreement.AgreementUtils.makeCodingStudy;
import static de.tudarmstadt.ukp.clarin.webanno.agreement.measures.ConcreteAgreementMeasure.COHEN_KAPPA_AGREEMENT;
import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.RELATION_TYPE;
import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.SPAN_TYPE;
import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.RELATION_TYPE;
import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.SPAN_TYPE;
import static java.util.Arrays.asList;
import static java.util.Collections.emptySet;
import static org.apache.uima.fit.factory.CollectionReaderFactory.createReader;
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import de.tudarmstadt.ukp.clarin.webanno.agreement.results.coding.CodingAgreementResult;
import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff;
import de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst;
import de.tudarmstadt.ukp.clarin.webanno.tsv.WebannoTsv2Reader;
import de.tudarmstadt.ukp.clarin.webanno.tsv.WebannoTsv3XReader;
import de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token;
import de.tudarmstadt.ukp.inception.support.WebAnnoConst;

public class AgreementTestUtils
{
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import de.tudarmstadt.ukp.clarin.webanno.diag.CasDoctorException;
import de.tudarmstadt.ukp.clarin.webanno.model.Project;
import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
import de.tudarmstadt.ukp.clarin.webanno.support.logging.BaseLoggers;
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.api.AnnotationSchemaService;
import de.tudarmstadt.ukp.inception.schema.api.event.LayerConfigurationChangedEvent;
import de.tudarmstadt.ukp.inception.support.logging.BaseLoggers;

/**
* <p>
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package de.tudarmstadt.ukp.inception.annotation.storage.driver.filesystem;

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 de.tudarmstadt.ukp.inception.support.logging.BaseLoggers.BOOT_LOG;
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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import de.tudarmstadt.ukp.clarin.webanno.api.casstorage.ConcurentCasModificationException;
import de.tudarmstadt.ukp.clarin.webanno.api.type.CASMetadata;
import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
import de.tudarmstadt.ukp.clarin.webanno.support.wicket.WicketUtil;
import de.tudarmstadt.ukp.inception.annotation.storage.CasMetadataUtils;
import de.tudarmstadt.ukp.inception.annotation.storage.CasStorageMetadata;
import de.tudarmstadt.ukp.inception.annotation.storage.config.CasStorageBackupProperties;
import de.tudarmstadt.ukp.inception.annotation.storage.config.CasStorageProperties;
import de.tudarmstadt.ukp.inception.annotation.storage.driver.CasStorageDriver;
import de.tudarmstadt.ukp.inception.documents.api.RepositoryProperties;
import de.tudarmstadt.ukp.inception.support.wicket.WicketUtil;

public class FileSystemCasStorageDriver
implements CasStorageDriver
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Expand Up @@ -24,9 +24,9 @@
import static de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasUpgradeMode.AUTO_CAS_UPGRADE;
import static de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasUpgradeMode.FORCE_CAS_UPGRADE;
import static de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasUpgradeMode.NO_CAS_UPGRADE;
import static de.tudarmstadt.ukp.clarin.webanno.support.WebAnnoConst.INITIAL_CAS_PSEUDO_USER;
import static de.tudarmstadt.ukp.inception.annotation.storage.CasMetadataUtils.getInternalTypeSystem;
import static de.tudarmstadt.ukp.inception.annotation.storage.CasStorageSession.openNested;
import static de.tudarmstadt.ukp.inception.support.WebAnnoConst.INITIAL_CAS_PSEUDO_USER;
import static java.lang.Thread.sleep;
import static java.util.Arrays.asList;
import static org.apache.commons.lang3.StringUtils.repeat;
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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;
import de.tudarmstadt.ukp.clarin.webanno.support.logging.Logging;
import de.tudarmstadt.ukp.inception.annotation.storage.config.CasStorageBackupProperties;
import de.tudarmstadt.ukp.inception.annotation.storage.config.CasStorageCachePropertiesImpl;
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;
import de.tudarmstadt.ukp.inception.support.logging.Logging;

public class CasStorageServiceImplTest
{
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5 changes: 5 additions & 0 deletions inception/inception-api-annotation/pom.xml
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<groupId>de.tudarmstadt.ukp.inception.app</groupId>
<artifactId>inception-constraints</artifactId>
</dependency>
<dependency>
<groupId>de.tudarmstadt.ukp.inception.app</groupId>
<artifactId>inception-support-bootstrap</artifactId>
</dependency>

<dependency>
<groupId>org.dkpro.core</groupId>
<artifactId>dkpro-core-api-segmentation-asl</artifactId>
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import org.apache.wicket.Component;

import de.tudarmstadt.ukp.clarin.webanno.api.annotation.page.AnnotationPageBase;
import de.tudarmstadt.ukp.clarin.webanno.support.extensionpoint.Extension;
import de.tudarmstadt.ukp.inception.support.extensionpoint.Extension;

public interface ActionBarExtension
extends Extension<AnnotationPageBase>
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