Package uk.ac.gda.vmxi.lims.api

Interface Lims

All Superinterfaces:

Findable

All Known Implementing Classes:

LimsAgentBase, LimsAgentDummy, LimsAgentMock, LimsAgentVmxi

public interface Lims
extends Findable

Interface for access to laboratory information systems describing the experimental session, samples and collection parameters. Compatible with ISPyB API v1.4

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)
Optional<PlateContext>	getPlateContext(String barcode)
List<PlateInfo>	getPlatesByStatus(PlateStatus status)
List<SleeveInfo>	getSleeves()
List<SleeveInfo>	getSleevesByLocation(Integer locationIndex)
Optional<Visit>	getVisit(String barcode)
Boolean	isConnected()	Tests the configured connection to data sources
Boolean	isPlateCompleted(String plate_barcode)
Boolean	isPlateScheduled(String plate_barcode)
boolean	isPlateTimedout()
void	reconnect()
Optional<CollectionGroup>	registerCollectionGroup(String plate_barcode, 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)
void	setPlateCompleted(String plate_barcode)
void	setPlateContext(String plate_barcode, PlateContext context)
void	setPlateStatus(String plate_barcode, PlateStatus status, Integer index)
void	setSleeveLocation(Integer sleeveId, Integer location, Timestamp timestamp)
void	timeoutPlate()
void	unqueuePlate(String plate_barcode)
Optional<Long>	updateCollectionGroup(CollectionGroup group)	Update the database with CollectionGroup attributes

Methods inherited from interface gda.factory.Findable

getName, setName

Method Details

getPlate

Optional<PlateInfo> getPlate(String barcode)
                      throws LimsException

Throws:

LimsException

getPlatesByStatus

List<PlateInfo> getPlatesByStatus(PlateStatus status)
                           throws LimsException

Throws:

LimsException

getPlateContext

Optional<PlateContext> getPlateContext(String barcode)
                                throws LimsException

Throws:

LimsException

getExperiments

List<Experiment> getExperiments(String barcode)
                         throws LimsException

Throws:

LimsException

getExperiments

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

Throws:

LimsException

getPendingExperiments

List<Experiment> getPendingExperiments(String barcode)
                                throws LimsException

Throws:

LimsException

getPendingExperiments

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

Throws:

LimsException

getNextPlate

List<PlateInfo> getNextPlate()
                      throws LimsException

Throws:

LimsException

getNextTwentyDegreePlate

List<PlateInfo> getNextTwentyDegreePlate()
                                  throws LimsException

Throws:

LimsException

getNextFourDegreePlate

List<PlateInfo> getNextFourDegreePlate()
                                throws LimsException

Throws:

LimsException

getVisit

Optional<Visit> getVisit(String barcode)
                  throws LimsException

Throws:

LimsException

getSleevesByLocation

List<SleeveInfo> getSleevesByLocation(Integer locationIndex)
                               throws LimsException

Throws:

LimsException

setSleeveLocation

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

Throws:

LimsException

getSleeves

List<SleeveInfo> getSleeves()
                     throws LimsException

Throws:

LimsException

disconnect

void disconnect()

reconnect

void reconnect()
        throws LimsException

Throws:

LimsException

isConnected

Boolean isConnected()

Tests the configured connection to data sources

Returns:

true for successful connection

isPlateCompleted

Boolean isPlateCompleted(String plate_barcode)
                  throws LimsException

Throws:

LimsException

isPlateScheduled

Boolean isPlateScheduled(String plate_barcode)
                  throws LimsException

Throws:

LimsException

registerCollectionGroup

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

Throws:

LimsException

registerExperiment

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

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

Returns:

optional containing the new or modified dataColllectionId

Throws:

LimsException

registerImageMatchResult

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

Throws:

LimsException

requestPostProcessing

void requestPostProcessing(DataCollectionId collection)
                    throws LimsException

Throws:

LimsException

setPlateCompleted

void setPlateCompleted(String plate_barcode)
                throws LimsException

Throws:

LimsException

setPlateContext

void setPlateContext(String plate_barcode,
 PlateContext context)
              throws LimsException

Throws:

LimsException

setPlateStatus

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

Throws:

LimsException

unqueuePlate

void unqueuePlate(String plate_barcode)
           throws LimsException

Throws:

LimsException

updateCollectionGroup

Optional<Long> updateCollectionGroup(CollectionGroup group)
                              throws LimsException

Update the database with CollectionGroup attributes

Parameters:

group - the bean of attributes - groupId is mandatory

Returns:

Optional - non-null if update succeeded

Throws:

LimsException

isPlateTimedout

boolean isPlateTimedout()
                 throws LimsException

Throws:

LimsException

timeoutPlate

void timeoutPlate()
           throws LimsException

Throws:

LimsException

clearPlateTimeout

void clearPlateTimeout()
                throws LimsException

Throws:

LimsException