Package gda.px.util

Class GDAISpyB

java.lang.Object

gda.factory.FindableBase

gda.px.util.GDAISpyB

All Implemented Interfaces:

Findable, ISpyB

public class GDAISpyB
extends FindableBase
implements ISpyB

ISpyB singleton with visit set automatically to the value from the metadata Synchronization of applications is achieved by the object using the Event mechanism to publish and receive events containing the name of the table changed and the id of the record effected.

Constructor Summary

Constructors

Constructor	Description
GDAISpyB()

Method Summary

Modifier and Type	Method	Description
List<dna.xml.ScreeningStrategySubWedge>	allChildSubWedgesFromScreeningId(int screeningId)
List<dna.xml.ScreeningStrategySubWedge>	allChildSubWedgesFromWedges(List<dna.xml.ScreeningStrategyWedge> screeningStrategyWedges)
List<dna.xml.ScreeningStrategyWedge>	allChildWedgesFromScreeningId(int screeningId)
static String	getCurrentTimeString()	Sets the start time for this data collection to the current time
String	getCurrentVisit()
static ISpyB	getInstance()
dna.xml.Aperture[]	retrieveAperturesUsingSize(double apertureSize)
dna.xml.Container[]	retrieveContainer(int containerId)
dna.xml.DataCollection	retrieveDataCollection(int dataCollectionId)
dna.xml.DataCollection[]	retrieveDataCollectionsForSample(int sampleId)
int[]	retrieveFluorescenceSpectrumIdsForSample(int sampleId)
dna.xml.Dbobject	retrieveImageQualityIndicators(int dataCollectionId, int imageNumber)
dna.xml.BLSample[]	retrieveSamples(int blSampleId)
dna.xml.Screening[]	retrieveScreeningsForSample(int sampleId)
void	setCurrentVisit(String visit)
void	setIspyB(ISpyB ispyB)
void	setName(String name)	Set or change the name of the object (as defined in XML).
void	setUseCurrentUserVisit(boolean useCurrentUserVisit)	To ensure the user only accesses those records in the database that are appropriate for his visit GDAISpyB needs to set the currentVsiit to either the users visit or the batonholder's visit.
int	storeAperture(dna.xml.Aperture aperture)
int	storeBLSample(dna.xml.BLSample blSample)
int	storeContainer(dna.xml.Container container)
int	storeCrystal(dna.xml.Crystal crystal)
int	storeDataCollection(dna.xml.DataCollection dc)	Deprecated.
int	storeDataCollection(dna.xml.DataCollection dc, String visit)	Requests the ISPyB server to store a data collection
int	storeDataCollectionGroup(dna.xml.DataCollectionGroup dcg)	Deprecated.
int	storeDataCollectionGroup(dna.xml.DataCollectionGroup dcg, String visit)	Requests the ISPyB server to store a data collection group
int	storeDiffractionPlan(dna.xml.DiffractionPlan diffractionPlan)
int	storeEnergyScan(dna.xml.EnergyScan energyScan)	Requests the ISPyB server to store an energy scan
int	storeFluorescenceSpectrum(dna.xml.XFEFluorescenceSpectrum fluoSpectrum)
int	storeGridInfo(dna.xml.GridInfo gridInfo)
int	storePosition(dna.xml.Position position)
int	storeProtein(dna.xml.Protein protein)
void	updateBLSample(dna.xml.BLSample blSample)
void	updateDataCollection(dna.xml.DataCollection dc)	Requests the ISPyB server to update a data collection.

Methods inherited from class gda.factory.FindableBase

equals, getName, hashCode

Methods inherited from class java.lang.Object

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

Constructor Details

GDAISpyB

public GDAISpyB()

Method Details

setUseCurrentUserVisit

public void setUseCurrentUserVisit(boolean useCurrentUserVisit)

To ensure the user only accesses those records in the database that are appropriate for his visit GDAISpyB needs to set the currentVsiit to either the users visit or the batonholder's visit. On the client the visit should be that of the local user.

Parameters:

useCurrentUserVisit - - when true, visit of the current user is used during database access. If false (default) visit of the baton holder is used. When GDAISpyB is in the client application this parameter should be set true

setIspyB

public void setIspyB(ISpyB ispyB)

Parameters:

ispyB -

getCurrentVisit

public String getCurrentVisit()

Specified by:

getCurrentVisit in interface ISpyB

Returns:

The visit set in setCurrentVisit e.g. nt20-14

retrieveContainer

public dna.xml.Container[] retrieveContainer(int containerId)
                                      throws ISPyBToolsException

Specified by:

retrieveContainer in interface ISpyB

Parameters:

containerId -

Returns:

Container[]

Throws:

ISPyBToolsException

retrieveDataCollection

public dna.xml.DataCollection retrieveDataCollection(int dataCollectionId)
                                              throws ISPyBToolsException

Specified by:

retrieveDataCollection in interface ISpyB

Parameters:

dataCollectionId -

Returns:

The dataCollections for the current Visit(session)

Throws:

ISPyBToolsException

retrieveSamples

public dna.xml.BLSample[] retrieveSamples(int blSampleId)
                                   throws ISPyBToolsException

Specified by:

retrieveSamples in interface ISpyB

Parameters:

blSampleId -

Returns:

BLSample

Throws:

ISPyBToolsException

setCurrentVisit

public void setCurrentVisit(String visit)
                     throws ISPyBToolsException

Specified by:

setCurrentVisit in interface ISpyB

Parameters:

visit -

Throws:

ISPyBToolsException

storeDataCollectionGroup

public int storeDataCollectionGroup(dna.xml.DataCollectionGroup dcg,
 String visit)
                             throws ISPyBToolsException

Description copied from interface: ISpyB

Requests the ISPyB server to store a data collection group

Specified by:

storeDataCollectionGroup in interface ISpyB

Parameters:

dcg - the DataCollectionGroup object

visit - string representing the visit with which to register dcg

Returns:

ID of inserted data collection group if the method terminates successfully, else -1

Throws:

ISPyBToolsException

storeDataCollectionGroup

@Deprecated(since="GDA 9.14")
public int storeDataCollectionGroup(dna.xml.DataCollectionGroup dcg)
                             throws ISPyBToolsException

Deprecated.

Specified by:

storeDataCollectionGroup in interface ISpyB

Throws:

ISPyBToolsException

storeDataCollection

public int storeDataCollection(dna.xml.DataCollection dc,
 String visit)
                        throws ISPyBToolsException

Description copied from interface: ISpyB

Requests the ISPyB server to store a data collection

Specified by:

storeDataCollection in interface ISpyB

Parameters:

dc - the DataCollection object

visit - string representing the visit with which to register dc

Returns:

ID of inserted data collection if the method terminates successfully, else -1

Throws:

ISPyBToolsException

storeDataCollection

@Deprecated(since="GDA 9.14")
public int storeDataCollection(dna.xml.DataCollection dc)
                        throws ISPyBToolsException

Deprecated.

Specified by:

storeDataCollection in interface ISpyB

Throws:

ISPyBToolsException

storeFluorescenceSpectrum

public int storeFluorescenceSpectrum(dna.xml.XFEFluorescenceSpectrum fluoSpectrum)
                              throws ISPyBToolsException

Specified by:

storeFluorescenceSpectrum in interface ISpyB

Throws:

ISPyBToolsException

updateDataCollection

public void updateDataCollection(dna.xml.DataCollection dc)
                          throws ISPyBToolsException

Description copied from interface: ISpyB

Requests the ISPyB server to update a data collection. Note that the dataCollectionId attribute has to be set correctly before running this method.

Specified by:

updateDataCollection in interface ISpyB

Parameters:

dc - the DataCollection object

Throws:

ISPyBToolsException

storeEnergyScan

public int storeEnergyScan(dna.xml.EnergyScan energyScan)
                    throws ISPyBToolsException

Description copied from interface: ISpyB

Requests the ISPyB server to store an energy scan

Specified by:

storeEnergyScan in interface ISpyB

Parameters:

energyScan -

Returns:

ID of inserted energy scan if the method terminates successfully, else -1

Throws:

ISPyBToolsException

storeBLSample

public int storeBLSample(dna.xml.BLSample blSample)
                  throws ISPyBToolsException

Specified by:

storeBLSample in interface ISpyB

Throws:

ISPyBToolsException

storeContainer

public int storeContainer(dna.xml.Container container)
                   throws ISPyBToolsException

Specified by:

storeContainer in interface ISpyB

Throws:

ISPyBToolsException

storeCrystal

public int storeCrystal(dna.xml.Crystal crystal)
                 throws ISPyBToolsException

Specified by:

storeCrystal in interface ISpyB

Throws:

ISPyBToolsException

storeProtein

public int storeProtein(dna.xml.Protein protein)
                 throws ISPyBToolsException

Specified by:

storeProtein in interface ISpyB

Throws:

ISPyBToolsException

updateBLSample

public void updateBLSample(dna.xml.BLSample blSample)
                    throws ISPyBToolsException

Specified by:

updateBLSample in interface ISpyB

Throws:

ISPyBToolsException

storeDiffractionPlan

public int storeDiffractionPlan(dna.xml.DiffractionPlan diffractionPlan)
                         throws ISPyBToolsException

Specified by:

storeDiffractionPlan in interface ISpyB

Throws:

ISPyBToolsException

setName

public void setName(String name)

Description copied from interface: Findable

Set or change the name of the object (as defined in XML).

Specified by:

setName in interface Findable

Overrides:

setName in class FindableBase

Parameters:

name - the object name

storeAperture

public int storeAperture(dna.xml.Aperture aperture)
                  throws ISPyBToolsException

Specified by:

storeAperture in interface ISpyB

Throws:

ISPyBToolsException

retrieveAperturesUsingSize

public dna.xml.Aperture[] retrieveAperturesUsingSize(double apertureSize)
                                              throws ISPyBToolsException

Specified by:

retrieveAperturesUsingSize in interface ISpyB

Throws:

ISPyBToolsException

storePosition

public int storePosition(dna.xml.Position position)
                  throws ISPyBToolsException

Specified by:

storePosition in interface ISpyB

Throws:

ISPyBToolsException

retrieveScreeningsForSample

public dna.xml.Screening[] retrieveScreeningsForSample(int sampleId)
                                                throws ISPyBToolsException

Specified by:

retrieveScreeningsForSample in interface ISpyB

Throws:

ISPyBToolsException

allChildSubWedgesFromScreeningId

public List<dna.xml.ScreeningStrategySubWedge> allChildSubWedgesFromScreeningId(int screeningId)
                                                                         throws ISPyBToolsException

Specified by:

allChildSubWedgesFromScreeningId in interface ISpyB

Throws:

ISPyBToolsException

allChildWedgesFromScreeningId

public List<dna.xml.ScreeningStrategyWedge> allChildWedgesFromScreeningId(int screeningId)
                                                                   throws ISPyBToolsException

Specified by:

allChildWedgesFromScreeningId in interface ISpyB

Throws:

ISPyBToolsException

allChildSubWedgesFromWedges

public List<dna.xml.ScreeningStrategySubWedge> allChildSubWedgesFromWedges(List<dna.xml.ScreeningStrategyWedge> screeningStrategyWedges)
                                                                    throws ISPyBToolsException

Specified by:

allChildSubWedgesFromWedges in interface ISpyB

Throws:

ISPyBToolsException

retrieveDataCollectionsForSample

public dna.xml.DataCollection[] retrieveDataCollectionsForSample(int sampleId)
                                                          throws ISPyBToolsException

Specified by:

retrieveDataCollectionsForSample in interface ISpyB

Throws:

ISPyBToolsException

retrieveFluorescenceSpectrumIdsForSample

public int[] retrieveFluorescenceSpectrumIdsForSample(int sampleId)
                                               throws ISPyBToolsException

Specified by:

retrieveFluorescenceSpectrumIdsForSample in interface ISpyB

Throws:

ISPyBToolsException

storeGridInfo

public int storeGridInfo(dna.xml.GridInfo gridInfo)
                  throws ISPyBToolsException

Specified by:

storeGridInfo in interface ISpyB

Throws:

ISPyBToolsException

retrieveImageQualityIndicators

public dna.xml.Dbobject retrieveImageQualityIndicators(int dataCollectionId,
 int imageNumber)
                                                throws ISPyBToolsException

Specified by:

retrieveImageQualityIndicators in interface ISpyB

Throws:

ISPyBToolsException

getInstance

public static ISpyB getInstance()

Returns:

ISpyB singleton with visit set automatically to the value from the metadata

getCurrentTimeString

public static String getCurrentTimeString()

Sets the start time for this data collection to the current time

Returns:

the current (Java VM) time as a string on a format acceptable by the ISPyB server