Class ArrayDesignReportServiceImpl

java.lang.Object

ubic.gemma.core.analysis.report.ArrayDesignReportServiceImpl

All Implemented Interfaces:

ArrayDesignReportService

@Component("arrayDesignReportService")
public class ArrayDesignReportServiceImpl
extends Object
implements ArrayDesignReportService

Author:

jsantos

Constructor Summary

Constructors

Constructor	Description
ArrayDesignReportServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	fillEventInformation(Collection<ArrayDesignValueObject> adVos)	Fill in event information
void	fillInSubsumptionInfo(Collection<ArrayDesignValueObject> valueObjects)
void	fillInValueObjects(Collection<ArrayDesignValueObject> adVos)	Fill in the probe summary statistics
void	generateAllArrayDesignReport()	Write the report summarizing all platforms.
void	generateArrayDesignReport()	Generate reports for all array designs, as well as the "global" report.
ArrayDesignValueObject	generateArrayDesignReport(Long id)	Generate the report for one platform, for callers that do so as a side effect of other work.
void	generateArrayDesignReport(ArrayDesignValueObject adVo)	Generate the report for one platform.
String	getCreateDate(Long id)
String	getLastGeneMappingEvent(Long id)
String	getLastRepeatMaskEvent(Long id)
String	getLastSequenceAnalysisEvent(Long id)
String	getLastSequenceUpdateEvent(Long id)
String	getReportDir()	Absolute directory the cached platform reports are read from and written to.
ArrayDesignValueObject	getSummaryObject()	Get the cached summary object that represents all platforms.
ArrayDesignValueObject	getSummaryObject(Long id)	Get a specific cached summary object
Collection<ArrayDesignValueObject>	getSummaryObject(Collection<Long> ids)	Get the cached summary objects

Methods inherited from class Object

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

Constructor Details

ArrayDesignReportServiceImpl

public ArrayDesignReportServiceImpl()

Method Details

getReportDir

public String getReportDir()

Description copied from interface: ArrayDesignReportService

Absolute directory the cached platform reports are read from and written to.

Exposed so callers can say where their output went. The path is derived from gemma.appdata.home, which differs between the CLI (running on the host) and gemma-rest (running in a container against a mounted volume) — a report written to the wrong one is invisible to the other with no error anywhere, which has already cost a debugging session.

Specified by:

getReportDir in interface ArrayDesignReportService

generateAllArrayDesignReport

public void generateAllArrayDesignReport()

Description copied from interface: ArrayDesignReportService

Write the report summarizing all platforms.

Specified by:

generateAllArrayDesignReport in interface ArrayDesignReportService

generateArrayDesignReport

@Secured("GROUP_AGENT")
public void generateArrayDesignReport()

Description copied from interface: ArrayDesignReportService

Generate reports for all array designs, as well as the "global" report.

A platform whose report cannot be written is logged and skipped.

Specified by:

generateArrayDesignReport in interface ArrayDesignReportService

generateArrayDesignReport

public void generateArrayDesignReport(ArrayDesignValueObject adVo)

Description copied from interface: ArrayDesignReportService

Generate the report for one platform.

Specified by:

generateArrayDesignReport in interface ArrayDesignReportService

generateArrayDesignReport

public ArrayDesignValueObject generateArrayDesignReport(Long id)

Description copied from interface: ArrayDesignReportService

Generate the report for one platform, for callers that do so as a side effect of other work.

A report that cannot be written is logged, not thrown, and the previous report is left in place. Use ArrayDesignReportService.generateArrayDesignReport(ArrayDesignValueObject) to find out whether the write succeeded.

Specified by:

generateArrayDesignReport in interface ArrayDesignReportService

Returns:

the report just written, or null if the platform has no value object or the report could not be written

getSummaryObject

public ArrayDesignValueObject getSummaryObject(Long id)

Get a specific cached summary object

Specified by:

getSummaryObject in interface ArrayDesignReportService

Returns:

arrayDesignValueObject the specified summary object

getSummaryObject

public ArrayDesignValueObject getSummaryObject()

Get the cached summary object that represents all platforms.

Specified by:

getSummaryObject in interface ArrayDesignReportService

Returns:

arrayDesignValueObject the summary object that represents the grand total of all array designs

getSummaryObject

public Collection<ArrayDesignValueObject> getSummaryObject(Collection<Long> ids)

Get the cached summary objects

Specified by:

getSummaryObject in interface ArrayDesignReportService

Returns:

arrayDesignValueObjects the specified summary object

fillEventInformation

public void fillEventInformation(Collection<ArrayDesignValueObject> adVos)

Fill in event information

Specified by:

fillEventInformation in interface ArrayDesignReportService

fillInSubsumptionInfo

public void fillInSubsumptionInfo(Collection<ArrayDesignValueObject> valueObjects)

Specified by:

fillInSubsumptionInfo in interface ArrayDesignReportService

fillInValueObjects

public void fillInValueObjects(Collection<ArrayDesignValueObject> adVos)

Fill in the probe summary statistics

Specified by:

fillInValueObjects in interface ArrayDesignReportService

getLastSequenceUpdateEvent

public String getLastSequenceUpdateEvent(Long id)

Specified by:

getLastSequenceUpdateEvent in interface ArrayDesignReportService

getLastSequenceAnalysisEvent

public String getLastSequenceAnalysisEvent(Long id)

Specified by:

getLastSequenceAnalysisEvent in interface ArrayDesignReportService

getLastRepeatMaskEvent

public String getLastRepeatMaskEvent(Long id)

Specified by:

getLastRepeatMaskEvent in interface ArrayDesignReportService

getLastGeneMappingEvent

public String getLastGeneMappingEvent(Long id)

Specified by:

getLastGeneMappingEvent in interface ArrayDesignReportService

getCreateDate

public String getCreateDate(Long id)

Specified by:

getCreateDate in interface ArrayDesignReportService