Class CliArrayDesignAuditServiceImpl

java.lang.Object

ubic.gemma.cli.audit.CliArrayDesignAuditServiceImpl

All Implemented Interfaces:

CliArrayDesignAuditService

@Service
public class CliArrayDesignAuditServiceImpl
extends Object
implements CliArrayDesignAuditService

Default CliArrayDesignAuditService implementation. Each method body is intentionally empty: the work is done by AuditedAspect, which picks up the @Audited annotation, locates the ArrayDesign argument, and writes the audit row through AuditTrailService. Resolving the audit note through messageSpel keeps the note verbatim from the caller's argument.

Lives under ubic.gemma.cli.audit so it is picked up by the stereotype scan declared in CliComponentScanConfig (the ubic.gemma.apps scan is restricted to CLI assignable types and would not include this co-bean).

The legacy private void audit(...) helpers in the CLI tools paired audit-event emission with an arrayDesignReportService.generateArrayDesignReport(...) call. The report refresh is preserved at the CALL site -- it has no relation to the audit event and stays in the CLI's own code path.

Constructor Summary

Constructors

Constructor	Description
CliArrayDesignAuditServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	recordAlignmentBasedGeneMapping(ArrayDesign arrayDesign, String note)	Records an AlignmentBasedGeneMappingEvent on the platform.
void	recordAnnotationBasedGeneMapping(ArrayDesign arrayDesign, String note)	Records an AnnotationBasedGeneMappingEvent on the platform.
void	recordProbeRenaming(ArrayDesign arrayDesign, String note)	Records an ArrayDesignProbeRenamingEvent on the platform.
void	recordRepeatAnalysis(ArrayDesign arrayDesign, String note)	Records an ArrayDesignRepeatAnalysisEvent on the platform.
void	recordSequenceAnalysis(ArrayDesign arrayDesign, String note)	Records an ArrayDesignSequenceAnalysisEvent on the platform.
void	recordSequenceRemove(ArrayDesign arrayDesign, String note)	Records an ArrayDesignSequenceRemoveEvent on the platform.
void	recordSequenceUpdate(ArrayDesign arrayDesign, String note)	Records an ArrayDesignSequenceUpdateEvent on the platform.
void	recordSubsumeCheck(ArrayDesign arrayDesign, String note)	Records an ArrayDesignSubsumeCheckEvent on the platform.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

CliArrayDesignAuditServiceImpl

public CliArrayDesignAuditServiceImpl()

Method Details

recordSequenceAnalysis

@Audited(value=ArrayDesignSequenceAnalysisEvent.class,
         messageSpel="#note")
public void recordSequenceAnalysis(ArrayDesign arrayDesign,
 String note)

Description copied from interface: CliArrayDesignAuditService

Records an ArrayDesignSequenceAnalysisEvent on the platform. Used by ArrayDesignBlatCli after a successful BLAT alignment pass (or after re-using results from a PSL file).

Specified by:

recordSequenceAnalysis in interface CliArrayDesignAuditService

recordSequenceUpdate

@Audited(value=ArrayDesignSequenceUpdateEvent.class,
         messageSpel="#note")
public void recordSequenceUpdate(ArrayDesign arrayDesign,
 String note)

Description copied from interface: CliArrayDesignAuditService

Records an ArrayDesignSequenceUpdateEvent on the platform. Used by ArrayDesignSequenceAssociationCli after attaching or looking up biological sequences for the platform's composite sequences.

Specified by:

recordSequenceUpdate in interface CliArrayDesignAuditService

recordSequenceRemove

@Audited(value=ArrayDesignSequenceRemoveEvent.class,
         messageSpel="#note")
public void recordSequenceRemove(ArrayDesign arrayDesign,
 String note)

Description copied from interface: CliArrayDesignAuditService

Records an ArrayDesignSequenceRemoveEvent on the platform. Used by ArrayDesignBioSequenceDetachCli after detaching the sequences associated with the platform.

Specified by:

recordSequenceRemove in interface CliArrayDesignAuditService

recordProbeRenaming

@Audited(value=ArrayDesignProbeRenamingEvent.class,
         messageSpel="#note")
public void recordProbeRenaming(ArrayDesign arrayDesign,
 String note)

Description copied from interface: CliArrayDesignAuditService

Records an ArrayDesignProbeRenamingEvent on the platform. Called after applying a probe-renaming map.

Specified by:

recordProbeRenaming in interface CliArrayDesignAuditService

recordRepeatAnalysis

@Audited(value=ArrayDesignRepeatAnalysisEvent.class,
         messageSpel="#note")
public void recordRepeatAnalysis(ArrayDesign arrayDesign,
 String note)

Description copied from interface: CliArrayDesignAuditService

Records an ArrayDesignRepeatAnalysisEvent on the platform. Used by ArrayDesignRepeatScanCli after running a repeat-masker scan over the platform's sequences.

Specified by:

recordRepeatAnalysis in interface CliArrayDesignAuditService

recordSubsumeCheck

@Audited(value=ArrayDesignSubsumeCheckEvent.class,
         messageSpel="#note")
public void recordSubsumeCheck(ArrayDesign arrayDesign,
 String note)

Description copied from interface: CliArrayDesignAuditService

Records an ArrayDesignSubsumeCheckEvent on the platform. Used by ArrayDesignSubsumptionTesterCli after testing whether the platform subsumes (or is subsumed by) other platforms.

Specified by:

recordSubsumeCheck in interface CliArrayDesignAuditService

recordAnnotationBasedGeneMapping

@Audited(value=AnnotationBasedGeneMappingEvent.class,
         messageSpel="#note")
public void recordAnnotationBasedGeneMapping(ArrayDesign arrayDesign,
 String note)

Description copied from interface: CliArrayDesignAuditService

Records an AnnotationBasedGeneMappingEvent on the platform. Used by GenericGenelistDesignGenerator after rebuilding the platform from a list of NCBI gene IDs.

Specified by:

recordAnnotationBasedGeneMapping in interface CliArrayDesignAuditService

recordAlignmentBasedGeneMapping

@Audited(value=AlignmentBasedGeneMappingEvent.class,
         messageSpel="#note")
public void recordAlignmentBasedGeneMapping(ArrayDesign arrayDesign,
 String note)

Description copied from interface: CliArrayDesignAuditService

Records an AlignmentBasedGeneMappingEvent on the platform. Used by ArrayDesignProbeMapperCli for runs whose gene mapping came from BLAT alignment / probe sequence analysis (the default mode and the batch path).

Specified by:

recordAlignmentBasedGeneMapping in interface CliArrayDesignAuditService