Add new event subclasses and improve auditing APIs

Add two abstract event types to easily identify events that affect the
needs attention and troubled flags.

Add new APIs for retrieving all the auditables that have an event of a
given type.

Use generic types.

gemma-core/src/main/java/ubic/gemma/core/analysis/report/ArrayDesignReportServiceImpl.java

@@ -28,15 +28,14 @@
 import org.springframework.security.access.annotation.Secured;
 import org.springframework.stereotype.Component;
 import ubic.basecode.util.FileTools;
-import ubic.gemma.model.common.auditAndSecurity.Auditable;
+import ubic.gemma.core.config.Settings;
 import ubic.gemma.model.common.auditAndSecurity.AuditEvent;
 import ubic.gemma.model.common.auditAndSecurity.eventType.*;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject;
 import ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventService;
 import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService;
 import ubic.gemma.persistence.util.EntityUtils;
-import ubic.gemma.core.config.Settings;
 
 import java.io.*;
 import java.util.*;
@@ -287,14 +286,14 @@ public void fillEventInformation( Collection<ArrayDesignValueObject> adVos ) {
 
         Map<Long, ArrayDesign> idMap = EntityUtils.getIdMap( arrayDesigns );
 
-        Map<Class<? extends AuditEventType>, Map<Auditable, AuditEvent>> events = auditEventService
+        Map<Class<? extends AuditEventType>, Map<ArrayDesign, AuditEvent>> events = auditEventService
                 .getLastEvents( arrayDesigns, typesToGet );
 
-        Map<Auditable, AuditEvent> geneMappingEvents = events.get( ArrayDesignGeneMappingEvent.class );
-        Map<Auditable, AuditEvent> sequenceUpdateEvents = events.get( ArrayDesignSequenceUpdateEvent.class );
-        Map<Auditable, AuditEvent> sequenceAnalysisEvents = events.get( ArrayDesignSequenceAnalysisEvent.class );
-        Map<Auditable, AuditEvent> repeatAnalysisEvents = events.get( ArrayDesignRepeatAnalysisEvent.class );
-        Map<Auditable, AuditEvent> creationEvents = auditEventService.getCreateEvents( arrayDesigns );
+        Map<ArrayDesign, AuditEvent> geneMappingEvents = events.get( ArrayDesignGeneMappingEvent.class );
+        Map<ArrayDesign, AuditEvent> sequenceUpdateEvents = events.get( ArrayDesignSequenceUpdateEvent.class );
+        Map<ArrayDesign, AuditEvent> sequenceAnalysisEvents = events.get( ArrayDesignSequenceAnalysisEvent.class );
+        Map<ArrayDesign, AuditEvent> repeatAnalysisEvents = events.get( ArrayDesignRepeatAnalysisEvent.class );
+        Map<ArrayDesign, AuditEvent> creationEvents = auditEventService.getCreateEvents( arrayDesigns );
 
         for ( ArrayDesignValueObject adVo : adVos ) {
 

gemma-core/src/main/java/ubic/gemma/core/analysis/report/ExpressionExperimentReportServiceImpl.java

@@ -32,8 +32,8 @@
 import org.springframework.transaction.annotation.Transactional;
 import ubic.gemma.core.visualization.ExperimentalDesignVisualizationService;
 import ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject;
-import ubic.gemma.model.common.auditAndSecurity.Auditable;
 import ubic.gemma.model.common.auditAndSecurity.AuditEvent;
+import ubic.gemma.model.common.auditAndSecurity.Auditable;
 import ubic.gemma.model.common.auditAndSecurity.eventType.*;
 import ubic.gemma.model.expression.experiment.BatchEffectType;
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
@@ -195,16 +195,16 @@ public void populateEventInformation( Collection<ExpressionExperimentDetailsValu
         Map<Long, Date> lastArrayDesignUpdates = expressionExperimentService.getLastArrayDesignUpdate( ees );
         Collection<Class<? extends AuditEventType>> typesToGet = Arrays.asList( eventTypes );
 
-        Map<Class<? extends AuditEventType>, Map<Auditable, AuditEvent>> events = this.getEvents( ees, typesToGet );
+        Map<Class<? extends AuditEventType>, Map<ExpressionExperiment, AuditEvent>> events = this.getEvents( ees, typesToGet );
 
-        Map<Auditable, AuditEvent> linkAnalysisEvents = events.get( LinkAnalysisEvent.class );
-        Map<Auditable, AuditEvent> missingValueAnalysisEvents = events.get( MissingValueAnalysisEvent.class );
-        Map<Auditable, AuditEvent> rankComputationEvents = events.get( ProcessedVectorComputationEvent.class );
+        Map<ExpressionExperiment, AuditEvent> linkAnalysisEvents = events.get( LinkAnalysisEvent.class );
+        Map<ExpressionExperiment, AuditEvent> missingValueAnalysisEvents = events.get( MissingValueAnalysisEvent.class );
+        Map<ExpressionExperiment, AuditEvent> rankComputationEvents = events.get( ProcessedVectorComputationEvent.class );
 
-        Map<Auditable, AuditEvent> differentialAnalysisEvents = events.get( DifferentialExpressionAnalysisEvent.class );
-        Map<Auditable, AuditEvent> batchFetchEvents = events.get( BatchInformationFetchingEvent.class );
-        Map<Auditable, AuditEvent> batchMissingEvents = events.get( BatchInformationMissingEvent.class );
-        Map<Auditable, AuditEvent> pcaAnalysisEvents = events.get( PCAAnalysisEvent.class );
+        Map<ExpressionExperiment, AuditEvent> differentialAnalysisEvents = events.get( DifferentialExpressionAnalysisEvent.class );
+        Map<ExpressionExperiment, AuditEvent> batchFetchEvents = events.get( BatchInformationFetchingEvent.class );
+        Map<ExpressionExperiment, AuditEvent> batchMissingEvents = events.get( BatchInformationMissingEvent.class );
+        Map<ExpressionExperiment, AuditEvent> pcaAnalysisEvents = events.get( PCAAnalysisEvent.class );
 
         Map<Long, Collection<AuditEvent>> sampleRemovalEvents = this.getSampleRemovalEvents( ees );
 
@@ -435,11 +435,9 @@ public void recalculateExperimentBatchInfo( ExpressionExperiment ee ) {
         }
     }
 
-    private Map<Class<? extends AuditEventType>, Map<Auditable, AuditEvent>> getEvents(
+    private Map<Class<? extends AuditEventType>, Map<ExpressionExperiment, AuditEvent>> getEvents(
             Collection<ExpressionExperiment> ees, Collection<Class<? extends AuditEventType>> types ) {
-
         return auditEventService.getLastEvents( ees, types );
-
     }
 
     private Map<Long, Collection<AuditEvent>> getSampleRemovalEvents( Collection<ExpressionExperiment> ees ) {

gemma-core/src/main/java/ubic/gemma/core/analysis/report/WhatsNewServiceImpl.java

@@ -215,11 +215,15 @@ private WhatsNew getReportAsAnonymousUser( Date date ) {
     private WhatsNew getReport( Date date ) {
         WhatsNew wn = new WhatsNew( date );
 
-        Collection<Auditable> updatedObjects = auditEventService.getUpdatedSinceDate( date );
+        Collection<Auditable> updatedObjects = new HashSet<>();
+        updatedObjects.addAll( auditEventService.getUpdatedSinceDate( ArrayDesign.class, date ) );
+        updatedObjects.addAll( auditEventService.getUpdatedSinceDate( ExpressionExperiment.class, date ) );
         wn.setUpdatedObjects( updatedObjects );
         WhatsNewServiceImpl.log.info( wn.getUpdatedObjects().size() + " updated objects since " + date );
 
-        Collection<Auditable> newObjects = auditEventService.getNewSinceDate( date );
+        Collection<Auditable> newObjects = new HashSet<>();
+        newObjects.addAll( auditEventService.getNewSinceDate( ArrayDesign.class, date ) );
+        newObjects.addAll( auditEventService.getNewSinceDate( ExpressionExperiment.class, date ) );
         wn.setNewObjects( newObjects );
         WhatsNewServiceImpl.log.info( wn.getNewObjects().size() + " new objects since " + date );
 

gemma-core/src/main/java/ubic/gemma/core/context/SpringContextUtils.java

@@ -27,8 +27,8 @@
 import org.springframework.context.support.AbstractXmlApplicationContext;
 import org.springframework.context.support.ClassPathXmlApplicationContext;
 import org.springframework.security.core.context.SecurityContextHolder;
-import ubic.gemma.core.util.BuildInfo;
 import ubic.gemma.core.config.Settings;
+import ubic.gemma.core.util.BuildInfo;
 
 import java.util.ArrayList;
 import java.util.Arrays;

gemma-core/src/main/java/ubic/gemma/model/common/auditAndSecurity/eventType/DoesNotNeedAttentionEvent.java

@@ -27,7 +27,7 @@
  *
  * @author Paul
  */
-public class DoesNotNeedAttentionEvent extends CurationDetailsEvent {
+public class DoesNotNeedAttentionEvent extends NeedsAttentionAlteringEvent {
 
     /**
      * The serial version UID of this class. Needed for serialization.

gemma-core/src/main/java/ubic/gemma/model/common/auditAndSecurity/eventType/NeedsAttentionAlteringEvent.java

@@ -0,0 +1,9 @@
+package ubic.gemma.model.common.auditAndSecurity.eventType;
+
+import ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails;
+
+/**
+ * Base class for events altering {@link CurationDetails#getNeedsAttention()}.
+ */
+public abstract class NeedsAttentionAlteringEvent extends CurationDetailsEvent {
+}

gemma-core/src/main/java/ubic/gemma/model/common/auditAndSecurity/eventType/NeedsAttentionEvent.java

@@ -28,7 +28,7 @@
  *
  * @author Paul
  */
-public class NeedsAttentionEvent extends CurationDetailsEvent {
+public class NeedsAttentionEvent extends NeedsAttentionAlteringEvent {
 
     /**
      * The serial version UID of this class. Needed for serialization.

gemma-core/src/main/java/ubic/gemma/model/common/auditAndSecurity/eventType/NotTroubledStatusFlagEvent.java

@@ -26,7 +26,7 @@
  *
  * @author Paul
  */
-public class NotTroubledStatusFlagEvent extends CurationDetailsEvent {
+public class NotTroubledStatusFlagEvent extends TroubledStatusFlagAlteringEvent {
 
     /**
      * The serial version UID of this class. Needed for serialization.

gemma-core/src/main/java/ubic/gemma/model/common/auditAndSecurity/eventType/TroubledStatusFlagAlteringEvent.java

@@ -0,0 +1,10 @@
+package ubic.gemma.model.common.auditAndSecurity.eventType;
+
+import ubic.gemma.model.common.auditAndSecurity.curation.CurationDetails;
+
+/**
+ * Base class for events that alter the {@link CurationDetails#getTroubled()} flag.
+ * @author poirigui
+ */
+public abstract class TroubledStatusFlagAlteringEvent extends CurationDetailsEvent {
+}

gemma-core/src/main/java/ubic/gemma/model/common/auditAndSecurity/eventType/TroubledStatusFlagEvent.java

@@ -26,7 +26,7 @@
  *
  * @author Paul
  */
-public class TroubledStatusFlagEvent extends CurationDetailsEvent {
+public class TroubledStatusFlagEvent extends TroubledStatusFlagAlteringEvent {
 
     /**
      * The serial version UID of this class. Needed for serialization.

gemma-core/src/main/java/ubic/gemma/persistence/service/common/auditAndSecurity/AuditEventDao.java

@@ -18,11 +18,12 @@
  */
 package ubic.gemma.persistence.service.common.auditAndSecurity;
 
-import ubic.gemma.model.common.auditAndSecurity.Auditable;
 import ubic.gemma.model.common.auditAndSecurity.AuditEvent;
+import ubic.gemma.model.common.auditAndSecurity.Auditable;
 import ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType;
 import ubic.gemma.persistence.service.BaseDao;
 
+import javax.annotation.Nullable;
 import java.util.Collection;
 import java.util.Date;
 import java.util.List;
@@ -35,47 +36,53 @@
 public interface AuditEventDao extends BaseDao<AuditEvent> {
 
     /**
-     * @param auditable auditable
-     * @return events for the given auditable.
+     * Obtain the audit events associated to a given auditable.
+     * <p>
+     * Events are sorted by date in ascending order.
      */
     List<AuditEvent> getEvents( Auditable auditable );
 
     /**
-     * @param auditable auditable
-     * @param type      type
-     * @return the last AuditEvent of the specified type from the given auditable.
+     * Obtain the creation events for the given auditables.
+     * <p>
+     * If an auditable has more than one creation event (which is in itself a bug), the earliest one is returned.
+     */
+    <T extends Auditable> Map<T, AuditEvent> getCreateEvents( Collection<T> auditables );
+
+    /**
+     * Obtain the latest event of a given type for a given auditable.
+     * @see #getLastEvent(Auditable, Class)
      */
+    @Nullable
     AuditEvent getLastEvent( Auditable auditable, Class<? extends AuditEventType> type );
 
     /**
-     * Obtain the latest {@link AuditEvent} of a specified type, excluding a certain number of types.
+     * Obtain the latest event of a given type, excluding a certain number of types.
+     * @param type          type of event to retrieve, augmented by its hierarchy
+     * @param excludedTypes excluded event types (their hierarchy is also excluded)
      */
+    @Nullable
     AuditEvent getLastEvent( Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes );
 
-    Map<Class<? extends AuditEventType>, Map<Auditable, AuditEvent>> getLastEventsByType(
-        Collection<? extends Auditable> auditables, Collection<Class<? extends AuditEventType>> types );
-
     /**
-     * Get auditables that have been Created since the given date
-     *
-     * @param date date
-     * @return auditables
+     * Obtain the latest events of a specified type for all given auditables.
+     * @see #getLastEvent(Auditable, Class)
      */
-    Collection<Auditable> getNewSinceDate( Date date );
+    <T extends Auditable> Map<T, AuditEvent> getLastEvents( Collection<T> auditables, Class<? extends AuditEventType> type );
 
     /**
-     * Get auditables that have been Updated since the given date
-     *
-     * @param date date
-     * @return auditables
+     * Obtain the latest events of a specified type for all auditable of a given type.
+     * @see #getLastEvent(Auditable, Class)
      */
-    Collection<Auditable> getUpdatedSinceDate( Date date );
+    <T extends Auditable> Map<T, AuditEvent> getLastEvents( Class<T> auditableClass, Class<? extends AuditEventType> type );
 
-    boolean hasEvent( Auditable a, Class<? extends AuditEventType> type );
-
-    void retainHavingEvent( Collection<? extends Auditable> a, Class<? extends AuditEventType> type );
-
-    void retainLackingEvent( Collection<? extends Auditable> a, Class<? extends AuditEventType> type );
+    /**
+     * Get auditables that have been created since the given date.
+     */
+    <T extends Auditable> Collection<T> getNewSinceDate( Class<T> auditableClass, Date date );
 
-    Map<Auditable, AuditEvent> getCreateEvents( Collection<? extends Auditable> auditables );
+    /**
+     * Get auditables that have been updated since the given date.
+     */
+    <T extends Auditable> Collection<T> getUpdatedSinceDate( Class<T> auditableClass, Date date );
 }