Uses of Class
ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType
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Uses of AuditEventType in ubic.gemma.core.apps
Method parameters in ubic.gemma.core.apps with type arguments of type AuditEventType Modifier and Type Method Description protected boolean
ExpressionExperimentManipulatingCLI. noNeedToRun(Auditable auditable, Class<? extends AuditEventType> eventClass)
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Uses of AuditEventType in ubic.gemma.core.util
Methods in ubic.gemma.core.util that return types with arguments of type AuditEventType Modifier and Type Method Description protected Class<? extends AuditEventType>
AbstractCLI. getAutoSeekEventType()
Method parameters in ubic.gemma.core.util with type arguments of type AuditEventType Modifier and Type Method Description protected void
AbstractCLI. addAutoOption(org.apache.commons.cli.Options options, Class<? extends AuditEventType> autoSeekEventType)
Add the-auto
option for a specificAuditEventType
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Uses of AuditEventType in ubic.gemma.model.common.auditAndSecurity
Methods in ubic.gemma.model.common.auditAndSecurity that return AuditEventType Modifier and Type Method Description AuditEventType
AuditEvent. getEventType()
AuditEventType
AuditEventValueObject. getEventType()
Methods in ubic.gemma.model.common.auditAndSecurity with parameters of type AuditEventType Modifier and Type Method Description static AuditEvent
AuditEvent.Factory. newInstance(Date date, AuditAction action, String note, String detail, User performer, AuditEventType eventType)
Create a new, immutable audit event.void
AuditEventValueObject. setEventType(AuditEventType eventType)
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Uses of AuditEventType in ubic.gemma.model.common.auditAndSecurity.eventType
Subclasses of AuditEventType in ubic.gemma.model.common.auditAndSecurity.eventType Modifier and Type Class Description class
AlignmentBasedGeneMappingEvent
Signifies a mapping based on sequence alignment performed by the system.class
AnalysisSuitabilityEvent
Used for indication of the suitability, or unsuitability, of an entity for a particular type of analysis.class
AnnotationBasedGeneMappingEvent
To signify the array design was mapped from an external source, not by our own sequence analysis.class
AnnotationEvent
class
ArrayDesignAnalysisEvent
An event involving the analysis of an ArrayDesignclass
ArrayDesignGeneMappingEvent
The mapping of probes to genes for an ArrayDesignclass
ArrayDesignMergeEvent
class
ArrayDesignProbeRenamingEvent
Signifies that the probes were renamed from their original values.class
ArrayDesignRepeatAnalysisEvent
class
ArrayDesignSequenceAnalysisEvent
The sequence alignment analysis of an ArrayDesignclass
ArrayDesignSequenceRemoveEvent
Used to indicate that all associations that this array design has with BioSequences have been removed.class
ArrayDesignSequenceUpdateEvent
The updating of the sequences associated with an ArrayDesignclass
ArrayDesignSubsumeCheckEvent
class
AutomatedAnnotationEvent
Deprecated.this event type was used by the auto-tagger, which has been removed.class
BatchCorrectionEvent
class
BatchInformationEvent
Abstract class for events related to batch information.class
BatchInformationFetchingEvent
Indicates that batch information was successfully obtained.class
BatchInformationMissingEvent
Indicate that batch information has been looked for and was missing.class
BatchProblemsUpdateEvent
Event that tracks when batch effects or problems are detected.class
BioMaterialMappingUpdate
To indicate that the biomaterial to bioassay mapping of the expression experiment was modified.class
CommentedEvent
An event indicating a comment was added to the auditable.class
CurationDetailsEvent
Event types that can changeCurationDetails
ofCuratable
objects.class
CurationNoteUpdateEvent
Indicates that previous validation is being invalidatedclass
DataAddedEvent
Indicates that a data type (for a specific QuantitationType, possibly new) was added.class
DataRemovedEvent
Indicates that a data type (for a specific QuantitationType, possibly new) was removed.class
DataReplacedEvent
Signifies that the data for the experiment was replaced (or filled in) after the experiment was loaded into the system.class
DifferentialExpressionAnalysisEvent
Indicates the experiment was the subject of a differential expression analysis.class
DifferentialExpressionSuitabilityEvent
Used to indicate the suitability status of an ExpressionExperiment for differential expression analysis.class
DoesNotNeedAttentionEvent
An event that occurs when a curator has validated the entity and indicated that it is "approved".class
ExperimentalDesignUpdatedEvent
Describes an event that involved a change of assignment of factor value to bio material, or other changes in the experimental design.class
ExpressionExperimentAnalysisEvent
An event involving an ExpressionExperimentclass
ExpressionExperimentPlatformSwitchEvent
The event that this expressionexperiment has had its array design switched (typically to a 'merged' one.class
ExpressionExperimentUpdateFromGEOEvent
Indicates that we have updated an expression experiment's information from GEO, after it was already loaded in Gemma.class
ExpressionExperimentVectorMergeEvent
Indicates that the "Vector merging" has been done on the associated experiment.class
FactorValueNeedsAttentionEvent
Indicates that a factor value needs attention.class
FailedBatchInformationFetchingEvent
Indicates that the attempt to get batch information failed due to an error.class
FailedBatchInformationMissingEvent
Deprecated.class
FailedDataReplacedEvent
Represents a failed data replace.class
FailedDifferentialExpressionAnalysisEvent
class
FailedLinkAnalysisEvent
class
FailedMeanVarianceUpdateEvent
class
FailedMissingValueAnalysisEvent
class
FailedPCAAnalysisEvent
class
FailedProcessedVectorComputationEvent
class
FailedSampleCorrelationAnalysisEvent
class
GeeqEvent
class
LinkAnalysisEvent
Computing coexpression links for an expression experimentclass
MakePrivateEvent
class
MakePublicEvent
class
ManualAnnotationEvent
class
MeanVarianceUpdateEvent
class
MissingValueAnalysisEvent
Computing missing values for an expression experimentclass
NeedsAttentionEvent
Indicates that previous validation is being invalidatedclass
NotTroubledStatusFlagEvent
This event type resets the trouble flag of curation details of a curatable object.class
OutlierAnalysisEvent
class
OutlierFoundAnalysisEvent
class
OutliersNotFoundAnalysisEvent
class
PCAAnalysisEvent
class
PermissionChangeEvent
Represents a change in permissionsclass
ProcessedVectorComputationEvent
Computation of the "processed" expression data with the ranking (by 'expression level') information filled in, for an Expression Experimentclass
RankComputationEvent
For backwards compatibility only.class
ReleaseDetailsUpdateEvent
Event triggered when the release details of aVersioned
entity are updated.class
ResetSuitabilityForDifferentialExpressionAnalysisEvent
Used to indicate that the suitability status of an experiment is the default.class
SampleCorrelationAnalysisEvent
class
SampleRemovalEvent
Event used when a sample is removed from an experiment (typically due to QC concerns or when marked as an outlier).class
SampleRemovalReversionEvent
Indicates that samples that were previously removed have been "put back", e.g.class
SingleBatchDeterminationEvent
Indicates that we got batch information, but there was (as far as we can tell) just one batch.class
SingletonBatchInvalidEvent
Indiates that there was at least one batch with only one sample.class
TooSmallDatasetLinkAnalysisEvent
Indicates that the data set had too few samples or probes to be analyzed (after filtering), and was skippedclass
TroubledStatusFlagEvent
Sets the trouble flag of curation details of any Curatable object.class
UninformativeFASTQHeadersForBatchingEvent
Indicates that FASTQ headers were present, but they were not usable for determining batches, typically because of invalid formatting or lack of information.class
UnsuitableForDifferentialExpressionAnalysisEvent
Indicates that the associated Experiment is NOT suitable for differential expression analysis.class
VersionedEvent
Base class for events relating to aVersioned
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Uses of AuditEventType in ubic.gemma.persistence.service.common.auditAndSecurity
Methods in ubic.gemma.persistence.service.common.auditAndSecurity that return types with arguments of type AuditEventType Modifier and Type Method Description Map<Class<? extends AuditEventType>,Map<Auditable,AuditEvent>>
AuditEventService. getLastEvents(Collection<? extends Auditable> auditables, Collection<Class<? extends AuditEventType>> types)
Fast method to retrieve auditEventTypes of multiple classes.Map<Class<? extends AuditEventType>,Map<Auditable,AuditEvent>>
AuditEventServiceImpl. getLastEvents(Collection<? extends Auditable> auditables, Collection<Class<? extends AuditEventType>> types)
Map<Class<? extends AuditEventType>,Map<Auditable,AuditEvent>>
AuditEventDao. getLastEventsByType(Collection<? extends Auditable> auditables, Collection<Class<? extends AuditEventType>> types)
Map<Class<? extends AuditEventType>,Map<Auditable,AuditEvent>>
AuditEventDaoImpl. getLastEventsByType(Collection<? extends Auditable> auditables, Collection<Class<? extends AuditEventType>> types)
Method parameters in ubic.gemma.persistence.service.common.auditAndSecurity with type arguments of type AuditEventType Modifier and Type Method Description AuditEvent
AuditTrailService. addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note)
AuditEvent
AuditTrailService. addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note, String detail)
AuditEvent
AuditTrailService. addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note, String detail, Date performedDate)
Add an update audit event of a specific type to the passed auditable entity.AuditEvent
AuditTrailService. addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note, Throwable throwable)
Add an update audit event with an exception.AuditEvent
AuditTrailServiceImpl. addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note)
AuditEvent
AuditTrailServiceImpl. addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note, String detail)
AuditEvent
AuditTrailServiceImpl. addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note, String detail, Date performedDate)
AuditEvent
AuditTrailServiceImpl. addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note, Throwable throwable)
This is using thePropagation.REQUIRES_NEW
so that if the throwable is raised, it will not roll back the audit trail event.AuditEvent
AuditEventDao. getLastEvent(Auditable auditable, Class<? extends AuditEventType> type)
AuditEvent
AuditEventDao. getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)
Obtain the latestAuditEvent
of a specified type, excluding a certain number of types.AuditEvent
AuditEventDao. getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)
Obtain the latestAuditEvent
of a specified type, excluding a certain number of types.AuditEvent
AuditEventDaoImpl. getLastEvent(Auditable auditable, Class<? extends AuditEventType> type)
AuditEvent
AuditEventDaoImpl. getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)
AuditEvent
AuditEventDaoImpl. getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)
AuditEvent
AuditEventService. getLastEvent(Auditable auditable, Class<? extends AuditEventType> type)
AuditEvent
AuditEventService. getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)
AuditEvent
AuditEventService. getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)
AuditEvent
AuditEventServiceImpl. getLastEvent(Auditable auditable, Class<? extends AuditEventType> type)
AuditEvent
AuditEventServiceImpl. getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)
AuditEvent
AuditEventServiceImpl. getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)
boolean
AuditEventDao. hasEvent(Auditable a, Class<? extends AuditEventType> type)
boolean
AuditEventDaoImpl. hasEvent(Auditable a, Class<? extends AuditEventType> type)
boolean
AuditEventService. hasEvent(Auditable a, Class<? extends AuditEventType> type)
boolean
AuditEventServiceImpl. hasEvent(Auditable a, Class<? extends AuditEventType> type)
void
AuditEventDao. retainHavingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void
AuditEventDaoImpl. retainHavingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void
AuditEventService. retainHavingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void
AuditEventServiceImpl. retainHavingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void
AuditEventDao. retainLackingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void
AuditEventDaoImpl. retainLackingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void
AuditEventService. retainLackingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void
AuditEventServiceImpl. retainLackingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
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