Package uk.ac.gda.vmxi.lims

Class LimsAgentVmxi

java.lang.Object

gda.factory.FindableBase

uk.ac.gda.vmxi.lims.LimsAgentBase

uk.ac.gda.vmxi.lims.LimsAgentVmxi

All Implemented Interfaces:

Findable, Lims

public class LimsAgentVmxi
extends LimsAgentBase
implements Lims

Field Summary

Fields

Modifier and Type	Field	Description
static final String	COMMAND_DATA_PROCESSING
static final String	TRIANGLE_NO_PLATE

Fields inherited from class uk.ac.gda.vmxi.lims.LimsAgentBase

PLATE_STATUSES_ALLOWED_FOR_LOCAL_STORAGE_INDEX_CHANGE

Constructor Summary

Constructors

Constructor	Description
LimsAgentVmxi()

Method Summary

Modifier and Type	Method	Description
void	clearPlateTimeout()
void	disconnect()
List<Experiment>	getExperiments(String barcode)
List<Experiment>	getExperiments(String barcode, String location)
List<PlateInfo>	getNextFourDegreePlate()
List<PlateInfo>	getNextPlate()
List<PlateInfo>	getNextTwentyDegreePlate()
List<Experiment>	getPendingExperiments(String barcode)
List<Experiment>	getPendingExperiments(String barcode, String location)
Optional<PlateInfo>	getPlate(String barcode)	Retrieve information stored about plate.
Optional<PlateContext>	getPlateContext(String barcode)
List<PlateInfo>	getPlatesByLocalStorageScheduled()	Retrieve list of scheduled plates in local storage
List<PlateInfo>	getPlatesByStatus(PlateStatus status)	Retrieve list of plates filtered by location or transit status
List<SleeveInfo>	getSleeves()
List<SleeveInfo>	getSleevesByLocation(Integer locationIndex)
Optional<Visit>	getVisit(String plateBarcode)
Boolean	isConnected()	Tests the configured connection to data sources
Boolean	isPlateCompleted(String plateBarcode)
Boolean	isPlateScheduled(String plateBarcode)
boolean	isPlateTimedout()
void	reconnect()
Optional<CollectionGroup>	registerCollectionGroup(String plateBarcode, String location, Timestamp startTime)
Optional<DataCollectionId>	registerExperiment(CollectionGroup group, DataCollectionRecord dataRec, Timestamp startTime, Timestamp endTime)	Register new data collection, or update a data collection by supplying the dataCollectionId
Optional<Long>	registerImageMatchResult(String barcode, String location, ImageMatchResult result)
void	requestPostProcessing(DataCollectionId collection)
static void	runProcessing(Long dataCollectionId)
void	setPlateCompleted(String plateBarcode)
void	setPlateContext(String plateBarcode, PlateContext plateContext)
void	setPlateStatus(String plateBarcode, PlateStatus status, Integer index)
void	setSleeveLocation(Integer sleeveId, Integer location, Timestamp timestamp)
void	timeoutPlate()
void	unqueuePlate(String plateBarcode)
Optional<Long>	updateCollectionGroup(CollectionGroup group)	Update the database with CollectionGroup attributes

Methods inherited from class gda.factory.FindableBase

equals, getName, hashCode, setName

Methods inherited from class java.lang.Object

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

Methods inherited from interface gda.factory.Findable

getName, setName

Field Details

COMMAND_DATA_PROCESSING

public static final String COMMAND_DATA_PROCESSING

See Also:

• Constant Field Values

TRIANGLE_NO_PLATE

public static final String TRIANGLE_NO_PLATE

See Also:

• Constant Field Values

Constructor Details

LimsAgentVmxi

public LimsAgentVmxi()

Method Details

runProcessing

public static void runProcessing(Long dataCollectionId)

getExperiments

public List<Experiment> getExperiments(String barcode)
                                throws LimsException

Specified by:

getExperiments in interface Lims

Throws:

LimsException

getExperiments

public List<Experiment> getExperiments(String barcode,
 String location)
                                throws LimsException

Specified by:

getExperiments in interface Lims

Throws:

LimsException

getPendingExperiments

public List<Experiment> getPendingExperiments(String barcode)
                                       throws LimsException

Specified by:

getPendingExperiments in interface Lims

Throws:

LimsException

getPendingExperiments

public List<Experiment> getPendingExperiments(String barcode,
 String location)
                                       throws LimsException

Specified by:

getPendingExperiments in interface Lims

Throws:

LimsException

getNextPlate

public List<PlateInfo> getNextPlate()
                             throws LimsException

Specified by:

getNextPlate in interface Lims

Throws:

LimsException

getNextTwentyDegreePlate

public List<PlateInfo> getNextTwentyDegreePlate()
                                         throws LimsException

Specified by:

getNextTwentyDegreePlate in interface Lims

Throws:

LimsException

getNextFourDegreePlate

public List<PlateInfo> getNextFourDegreePlate()
                                       throws LimsException

Specified by:

getNextFourDegreePlate in interface Lims

Throws:

LimsException

getPlate

public Optional<PlateInfo> getPlate(String barcode)
                             throws LimsException

Retrieve information stored about plate. To date, this does not retrieve the status timestamp - use getPlateContext() for that

Specified by:

getPlate in interface Lims

Throws:

LimsException

getPlateContext

public Optional<PlateContext> getPlateContext(String barcode)
                                       throws LimsException

Specified by:

getPlateContext in interface Lims

Throws:

LimsException

getPlatesByLocalStorageScheduled

public List<PlateInfo> getPlatesByLocalStorageScheduled()
                                                 throws LimsException

Retrieve list of scheduled plates in local storage

Returns:

list of plates

Throws:

LimsException

getPlatesByStatus

public List<PlateInfo> getPlatesByStatus(PlateStatus status)
                                  throws LimsException

Retrieve list of plates filtered by location or transit status

Specified by:

getPlatesByStatus in interface Lims

Parameters:

status - location or transit status on which to filter

Returns:

list of plates

Throws:

LimsException

getVisit

public Optional<Visit> getVisit(String plateBarcode)
                         throws LimsException

Specified by:

getVisit in interface Lims

Throws:

LimsException

getSleevesByLocation

public List<SleeveInfo> getSleevesByLocation(Integer locationIndex)
                                      throws LimsException

Specified by:

getSleevesByLocation in interface Lims

Throws:

LimsException

getSleeves

public List<SleeveInfo> getSleeves()
                            throws LimsException

Specified by:

getSleeves in interface Lims

Throws:

LimsException

setSleeveLocation

public void setSleeveLocation(Integer sleeveId,
 Integer location,
 Timestamp timestamp)
                       throws LimsException

Specified by:

setSleeveLocation in interface Lims

Throws:

LimsException

disconnect

public void disconnect()

Specified by:

disconnect in interface Lims

reconnect

public void reconnect()
               throws LimsException

Specified by:

reconnect in interface Lims

Throws:

LimsException

isConnected

public Boolean isConnected()

Description copied from interface: Lims

Tests the configured connection to data sources

Specified by:

isConnected in interface Lims

Returns:

true for successful connection

isPlateCompleted

public Boolean isPlateCompleted(String plateBarcode)
                         throws LimsException

Specified by:

isPlateCompleted in interface Lims

Throws:

LimsException

isPlateScheduled

public Boolean isPlateScheduled(String plateBarcode)
                         throws LimsException

Specified by:

isPlateScheduled in interface Lims

Throws:

LimsException

registerCollectionGroup

public Optional<CollectionGroup> registerCollectionGroup(String plateBarcode,
 String location,
 Timestamp startTime)
                                                  throws LimsException

Specified by:

registerCollectionGroup in interface Lims

Throws:

LimsException

registerExperiment

public Optional<DataCollectionId> registerExperiment(CollectionGroup group,
 DataCollectionRecord dataRec,
 Timestamp startTime,
 Timestamp endTime)
                                              throws LimsException

Description copied from interface: Lims

Register new data collection, or update a data collection by supplying the dataCollectionId

Specified by:

registerExperiment in interface Lims

Returns:

optional containing the new or modified dataColllectionId

Throws:

LimsException

registerImageMatchResult

public Optional<Long> registerImageMatchResult(String barcode,
 String location,
 ImageMatchResult result)
                                        throws LimsException

Specified by:

registerImageMatchResult in interface Lims

Throws:

LimsException

requestPostProcessing

public void requestPostProcessing(DataCollectionId collection)
                           throws LimsException

Specified by:

requestPostProcessing in interface Lims

Throws:

LimsException

setPlateCompleted

public void setPlateCompleted(String plateBarcode)
                       throws LimsException

Specified by:

setPlateCompleted in interface Lims

Throws:

LimsException

setPlateContext

public void setPlateContext(String plateBarcode,
 PlateContext plateContext)
                     throws LimsException

Specified by:

setPlateContext in interface Lims

Throws:

LimsException

setPlateStatus

public void setPlateStatus(String plateBarcode,
 PlateStatus status,
 Integer index)
                    throws LimsException

Specified by:

setPlateStatus in interface Lims

Throws:

LimsException

unqueuePlate

public void unqueuePlate(String plateBarcode)
                  throws LimsException

Specified by:

unqueuePlate in interface Lims

Throws:

LimsException

updateCollectionGroup

public Optional<Long> updateCollectionGroup(CollectionGroup group)
                                     throws LimsException

Description copied from interface: Lims

Update the database with CollectionGroup attributes

Specified by:

updateCollectionGroup in interface Lims

Parameters:

group - the bean of attributes - groupId is mandatory

Returns:

Optional - non-null if update succeeded

Throws:

LimsException

timeoutPlate

public void timeoutPlate()

Specified by:

timeoutPlate in interface Lims

clearPlateTimeout

public void clearPlateTimeout()

Specified by:

clearPlateTimeout in interface Lims

isPlateTimedout

public boolean isPlateTimedout()

Specified by:

isPlateTimedout in interface Lims