uk.ac.cisban.rod.dao
Class Find

java.lang.Object
  extended by uk.ac.cisban.rod.dao.Find

public class Find
extends java.lang.Object

For checking for and retrieving objects in the database.

Since:
07-Oct-2009, 14:12:29
Author:
Morgan Taschuk

Constructor Summary
Find(DAO dao)
          Even though DAO is a singleton, we pass to the constructor to avoid an infinite recursion.
 
Method Summary
 java.util.Map<java.lang.String,java.lang.Exception> fillPlateList(javax.jdo.PersistenceManager pm, java.util.List<java.lang.String> barcodes, java.util.List<Plate> listToFill)
          Fills the given list using the given barcodes with Plates from the DB.
 ActionApplication findActionApplication(javax.jdo.PersistenceManager pm, long identifier)
          Finds a ActionApplication given its database id.
 ActionCV findActionCV(javax.jdo.PersistenceManager pm, java.lang.Long id)
          Finds a ActionCV given its database id.
 ActionCV findActionCV(javax.jdo.PersistenceManager pm, java.lang.String identifier)
          Finds an ActionCV given its XML identifier .
 BackgroundMutationCV findBackgroundMutationCV(javax.jdo.PersistenceManager pm, java.lang.String mutationName)
          Finds a background mutation CV given its name.
 Barcode findBarcode(javax.jdo.PersistenceManager pm, long id)
          Finds a Barcode given its database id .
 Barcode findBarcode(javax.jdo.PersistenceManager pm, java.lang.String barcode)
          Finds a Barcode given its barcode String.
 EquipmentCV findEquipmentCV(javax.jdo.PersistenceManager pm, java.lang.String identifier)
          Finds an EquipmentCV given its FuGE identifier.
 Experiment findExperiment(javax.jdo.PersistenceManager pm, long id)
          Finds a Experiment given its database id.
 Experiment findExperiment(javax.jdo.PersistenceManager pm, java.lang.String name)
          Finds a Experiment given its name.
 FeatureCV findFeatureCV(javax.jdo.PersistenceManager pm, java.lang.String featureName)
          Finds a FeatureCV given its name.
 Image findImage(javax.jdo.PersistenceManager pm, java.lang.String uri)
          Finds an Image given its URI.
 ImageCV findImageCV(javax.jdo.PersistenceManager pm, java.lang.String description)
          Finds an ImageCV given its description.
 java.util.Collection<Image> findImages(javax.jdo.PersistenceManager pm, java.lang.Long barcodeId)
          Finds a collection of Images given their barcode database id .
 java.util.Collection<ImageSpot> findImageSpot(javax.jdo.PersistenceManager pm, java.lang.Long sourcePlatePosition)
          Finds a ImageSpot given its source PlatePosition database id.
 ImageTransformationCV findImageTransformationCV(javax.jdo.PersistenceManager pm, java.lang.String name)
          Finds a ImageTransformationCV given its name.
 Inoculation findInoculation(javax.jdo.PersistenceManager pm, java.lang.Long sourcePlatePosition, java.lang.Long destinationPlatePosition)
          Finds a Inoculation given its source and destination PlatePosition DB ids.
 java.util.Collection<Inoculation> findInoculationWithDestination(javax.jdo.PersistenceManager pm, java.lang.Long destinationPlatePosition)
          Finds a collection of Inoculations given their destination PlatePosition ids.
 Masterplate findMasterplate(javax.jdo.PersistenceManager pm, java.lang.String barcode)
          Locates a Plate in the database, given a barcode String.
 MasterplateLibraryCV findMasterplateLibraryCV(javax.jdo.PersistenceManager pm, java.lang.String name)
          Finds a MasterplateLibraryCV given its name.
 MasterplatePosition findMasterplatePosition(javax.jdo.PersistenceManager pm, java.lang.Long masterplateId, int row, int column)
          Finds a MasterplatePosition given its masterplate database id and row and column on the plate.
 MasterplateSet findMasterplateSet(javax.jdo.PersistenceManager pm, java.lang.Long id)
          Finds a MasterplateSet given its database id .
 MasterplateSet findMasterplateSet(javax.jdo.PersistenceManager pm, java.lang.String description)
          Finds a MasterplateSet given its description.
 MediumCV findMediumCV(javax.jdo.PersistenceManager pm, java.lang.Long id)
          Finds a MediumCV given its database id .
 MediumCV findMediumCV(javax.jdo.PersistenceManager pm, java.lang.String name)
          Finds a MediumCV given its name.
 java.lang.String findORF(javax.jdo.PersistenceManager pm, java.lang.Long masterplateId, java.lang.Long positionId)
          Finds an ORF given its masterplate database id and position database id.
 Plate findPlate(javax.jdo.PersistenceManager pm, java.lang.Long id)
          Finds a Plate given its database id .
 Plate findPlate(javax.jdo.PersistenceManager pm, java.lang.String barcode)
          Locates a Plate in the database, given a barcode String.
 PlateCV findPlateCV(javax.jdo.PersistenceManager pm, long id)
          Finds a PlateCV given its database id .
 PlateCV findPlateCV(javax.jdo.PersistenceManager pm, java.lang.String name)
          Finds a PlateCV given its name.
 PlatePosition findPlatePosition(javax.jdo.PersistenceManager pm, java.lang.Long id)
          Finds a PlatePosition given its DB id.
 PlatePosition findPlatePosition(javax.jdo.PersistenceManager pm, java.lang.Long barcodeId, java.lang.Long positionId)
          Finds a PlatePosition given its Barcode and Position DB ids.
 PlatePosition findPlatePosition(javax.jdo.PersistenceManager pm, java.lang.String barcode, int row, int column)
          Finds a PlatePosition given its Barcode value and row and column position.
 PlatePosition findPlatePosition(javax.jdo.PersistenceManager pm, java.lang.String barcode, java.lang.Long positionId)
          Finds a PlatePosition given its Barcode value and Position DB id.
 Position findPosition(javax.jdo.PersistenceManager pm, int row, int column)
          Finds a Position given its row and column.
 ProtocolApplication findProtocolApplication(javax.jdo.PersistenceManager pm, long id)
          Finds a ProtocolApplication given its database id.
 ProtocolCV findProtocolCV(javax.jdo.PersistenceManager pm, java.lang.Long id)
          Finds a ProtocolCV given its database id .
 ProtocolCV findProtocolCV(javax.jdo.PersistenceManager pm, java.lang.String identifier)
          Finds a ProtocolCV given its database id.
 Repeat findRepeat(javax.jdo.PersistenceManager pm, long id)
          Finds a Repeat given its database id.
protected  java.util.Collection<Repeat> findRepeats(javax.jdo.PersistenceManager pm, Experiment exp)
          Gets all repeats for a given experiment using experiment id as an identifier.
protected  java.util.Collection<Repeat> findRepeats(javax.jdo.PersistenceManager pm, long id)
          Gets all repeats for a given experiment using experiment id as an identifier.
 ActionApplication findSpotLogs(javax.jdo.PersistenceManager pm, long actionApplicationId)
          Finds spot logs given an action application database id.
 Spotting findSpotting(javax.jdo.PersistenceManager pm, java.lang.Long sourcePlatePosition, java.lang.Long destinationPlatePosition)
          Finds a Spotting given its source and destination PlatePosition DB ids.
 java.util.Collection<Spotting> findSpottingWithDestination(javax.jdo.PersistenceManager pm, java.lang.Long destinationPlatePosition)
          Finds a collection of Spottings given their destination PlatePosition DB id.
 int findTimeseriesOrder(javax.jdo.PersistenceManager pm, Image image)
          Finds the number of an image part of a series of images taken of the same plate.
 TreatmentCV findTreatmentCV(javax.jdo.PersistenceManager pm, java.lang.Long id)
          Finds a TreatmentCV given its database id .
 TreatmentCV findTreatmentCV(javax.jdo.PersistenceManager pm, java.lang.String name)
          Finds a TreatmentCV given its name.
 PlatePosition forceFindPlatePosition(javax.jdo.PersistenceManager pm, long barcodeId, int row, int column)
          Finds or creates a PlatePosition given its Barcode DB id and row and column.
 PlatePosition forceFindPlatePosition(javax.jdo.PersistenceManager pm, java.lang.String barcode, int row, int column)
          Finds or creates a PlatePosition given its Barcode value and row and column .
 Position forceFindPosition(javax.jdo.PersistenceManager pm, int row, int column)
          Finds a Position given its row and column.
 boolean mediumExists(javax.jdo.PersistenceManager pm, java.lang.String medName)
          Checks if a mediumCV exists.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Find

public Find(DAO dao)
Even though DAO is a singleton, we pass to the constructor to avoid an infinite recursion. This class should only be instantiated through the DAO.

Parameters:
dao - the database access object.
Method Detail

findTimeseriesOrder

public int findTimeseriesOrder(javax.jdo.PersistenceManager pm,
                               Image image)
                        throws QueryNotFoundException
Finds the number of an image part of a series of images taken of the same plate.

Parameters:
pm - persistence manager
image - the image to find the timeseries order or
Returns:
the ordering of the image in the timeseries; -1 if the image does not exist in the timeseries of the barcoded plate
Throws:
QueryNotFoundException - if there are no images of the barcoded plate

findBackgroundMutationCV

public BackgroundMutationCV findBackgroundMutationCV(javax.jdo.PersistenceManager pm,
                                                     java.lang.String mutationName)
                                              throws QueryNotFoundException
Finds a background mutation CV given its name.

Parameters:
pm - the persistence manager
mutationName -
Returns:
Throws:
QueryNotFoundException

findFeatureCV

public FeatureCV findFeatureCV(javax.jdo.PersistenceManager pm,
                               java.lang.String featureName)
                        throws QueryNotFoundException
Finds a FeatureCV given its name.

Parameters:
pm - the persistence manager
featureName - the name
Returns:
Throws:
QueryNotFoundException

findImage

public Image findImage(javax.jdo.PersistenceManager pm,
                       java.lang.String uri)
                throws QueryNotFoundException
Finds an Image given its URI.

Parameters:
pm - the persistence manager
uri - the URI of the image
Returns:
Throws:
QueryNotFoundException

findImages

public java.util.Collection<Image> findImages(javax.jdo.PersistenceManager pm,
                                              java.lang.Long barcodeId)
                                       throws QueryNotFoundException
Finds a collection of Images given their barcode database id .

Parameters:
pm - the persistence manager
barcodeId - the database id of the barcode
Returns:
Throws:
QueryNotFoundException

findImageCV

public ImageCV findImageCV(javax.jdo.PersistenceManager pm,
                           java.lang.String description)
                    throws QueryNotFoundException
Finds an ImageCV given its description.

Parameters:
pm - the persistence manager
description - the description
Returns:
Throws:
QueryNotFoundException

findImageTransformationCV

public ImageTransformationCV findImageTransformationCV(javax.jdo.PersistenceManager pm,
                                                       java.lang.String name)
                                                throws QueryNotFoundException
Finds a ImageTransformationCV given its name.

Parameters:
pm - the persistence manager
name - the name
Returns:
Throws:
QueryNotFoundException

findMasterplateLibraryCV

public MasterplateLibraryCV findMasterplateLibraryCV(javax.jdo.PersistenceManager pm,
                                                     java.lang.String name)
                                              throws QueryNotFoundException
Finds a MasterplateLibraryCV given its name.

Parameters:
pm - the persistence manager
name - the name
Returns:
Throws:
QueryNotFoundException

findMediumCV

public MediumCV findMediumCV(javax.jdo.PersistenceManager pm,
                             java.lang.String name)
                      throws QueryNotFoundException
Finds a MediumCV given its name.

Parameters:
pm - the persistence manager
name - the name
Returns:
Throws:
QueryNotFoundException

findMediumCV

public MediumCV findMediumCV(javax.jdo.PersistenceManager pm,
                             java.lang.Long id)
                      throws QueryNotFoundException
Finds a MediumCV given its database id .

Parameters:
pm - the persistence manager
id - the database id
Returns:
Throws:
QueryNotFoundException

mediumExists

public boolean mediumExists(javax.jdo.PersistenceManager pm,
                            java.lang.String medName)
                     throws QueryNotFoundException
Checks if a mediumCV exists.

Parameters:
pm - instance of a performance manager
medName - name of medium to locate
Returns:
true if medium cv exists, false if QueryNotFoundException.
Throws:
QueryNotFoundException - thrown if medium not found so returns false.

findPlateCV

public PlateCV findPlateCV(javax.jdo.PersistenceManager pm,
                           java.lang.String name)
                    throws QueryNotFoundException
Finds a PlateCV given its name.

Parameters:
pm - the persistence manager
name - the name
Returns:
Throws:
QueryNotFoundException

findPlateCV

public PlateCV findPlateCV(javax.jdo.PersistenceManager pm,
                           long id)
                    throws QueryNotFoundException
Finds a PlateCV given its database id .

Parameters:
pm - the persistence manager
id - the database id
Returns:
Throws:
QueryNotFoundException

findTreatmentCV

public TreatmentCV findTreatmentCV(javax.jdo.PersistenceManager pm,
                                   java.lang.String name)
                            throws QueryNotFoundException
Finds a TreatmentCV given its name.

Parameters:
pm - the persistence manager
name - the name
Returns:
Throws:
QueryNotFoundException

findTreatmentCV

public TreatmentCV findTreatmentCV(javax.jdo.PersistenceManager pm,
                                   java.lang.Long id)
                            throws QueryNotFoundException
Finds a TreatmentCV given its database id .

Parameters:
pm - the persistence manager
id - the database id of the TreatmentCV
Returns:
Throws:
QueryNotFoundException

findBarcode

public Barcode findBarcode(javax.jdo.PersistenceManager pm,
                           long id)
                    throws QueryNotFoundException
Finds a Barcode given its database id .

Parameters:
pm - the persistence manager
id - the database id of the Barcode
Returns:
Throws:
QueryNotFoundException

findBarcode

public Barcode findBarcode(javax.jdo.PersistenceManager pm,
                           java.lang.String barcode)
                    throws QueryNotFoundException
Finds a Barcode given its barcode String.

Parameters:
pm - the persistence manager
barcode - the Barcode value
Returns:
Throws:
QueryNotFoundException

findPlate

public Plate findPlate(javax.jdo.PersistenceManager pm,
                       java.lang.String barcode)
                throws QueryNotFoundException
Locates a Plate in the database, given a barcode String.

Parameters:
pm - the persistence manager
barcode - the String identifier of the barcode
Returns:
a Plate with the given Barcode string
Throws:
QueryNotFoundException - if either the Plate or the Barcode can't be found

findMasterplate

public Masterplate findMasterplate(javax.jdo.PersistenceManager pm,
                                   java.lang.String barcode)
                            throws QueryNotFoundException
Locates a Plate in the database, given a barcode String.

Parameters:
pm - the persistence manager
barcode - the String identifier of the barcode
Returns:
a Plate with the given Barcode string
Throws:
QueryNotFoundException - if either the Plate or the Barcode can't be found

findORF

public java.lang.String findORF(javax.jdo.PersistenceManager pm,
                                java.lang.Long masterplateId,
                                java.lang.Long positionId)
                         throws QueryNotFoundException
Finds an ORF given its masterplate database id and position database id.

Parameters:
pm - the persistence manager
masterplateId -
positionId -
Returns:
Throws:
QueryNotFoundException

findMasterplatePosition

public MasterplatePosition findMasterplatePosition(javax.jdo.PersistenceManager pm,
                                                   java.lang.Long masterplateId,
                                                   int row,
                                                   int column)
                                            throws QueryNotFoundException
Finds a MasterplatePosition given its masterplate database id and row and column on the plate.

Parameters:
pm - the persistence manager
masterplateId -
row -
column -
Returns:
Throws:
QueryNotFoundException

findPlate

public Plate findPlate(javax.jdo.PersistenceManager pm,
                       java.lang.Long id)
                throws QueryNotFoundException
Finds a Plate given its database id .

Parameters:
pm - the persistence manager
id - the database id of the Plate
Returns:
Throws:
QueryNotFoundException

findEquipmentCV

public EquipmentCV findEquipmentCV(javax.jdo.PersistenceManager pm,
                                   java.lang.String identifier)
                            throws QueryNotFoundException
Finds an EquipmentCV given its FuGE identifier.

Parameters:
pm - the persistence manager
identifier - the FuGE identifier of the EquipmentCV
Returns:
Throws:
QueryNotFoundException

findMasterplateSet

public MasterplateSet findMasterplateSet(javax.jdo.PersistenceManager pm,
                                         java.lang.String description)
                                  throws QueryNotFoundException
Finds a MasterplateSet given its description.

Parameters:
pm - the persistence manager
description - the description of the MasterplateSet
Returns:
Throws:
QueryNotFoundException

findMasterplateSet

public MasterplateSet findMasterplateSet(javax.jdo.PersistenceManager pm,
                                         java.lang.Long id)
                                  throws QueryNotFoundException
Finds a MasterplateSet given its database id .

Parameters:
pm - the persistence manager
id - the database id of the MasterplateSet
Returns:
Throws:
QueryNotFoundException

findProtocolCV

public ProtocolCV findProtocolCV(javax.jdo.PersistenceManager pm,
                                 java.lang.String identifier)
                          throws QueryNotFoundException
Finds a ProtocolCV given its database id.

Parameters:
pm - the persistence manager
identifier - the database id of the ProtocolCV
Returns:
Throws:
QueryNotFoundException

findProtocolCV

public ProtocolCV findProtocolCV(javax.jdo.PersistenceManager pm,
                                 java.lang.Long id)
                          throws QueryNotFoundException
Finds a ProtocolCV given its database id .

Parameters:
pm - the persistence manager
id - the database id of the ProtocolCV
Returns:
Throws:
QueryNotFoundException

findProtocolApplication

public ProtocolApplication findProtocolApplication(javax.jdo.PersistenceManager pm,
                                                   long id)
                                            throws QueryNotFoundException
Finds a ProtocolApplication given its database id.

Parameters:
pm - the persistence manager
id - the database id of the ProtocolApplication
Returns:
a ProtocolApplication
Throws:
QueryNotFoundException

findActionCV

public ActionCV findActionCV(javax.jdo.PersistenceManager pm,
                             java.lang.String identifier)
                      throws QueryNotFoundException
Finds an ActionCV given its XML identifier .

Parameters:
pm - the persistence manager
identifier - the XML identifier of the ActionCV
Returns:
Throws:
QueryNotFoundException

findActionCV

public ActionCV findActionCV(javax.jdo.PersistenceManager pm,
                             java.lang.Long id)
                      throws QueryNotFoundException
Finds a ActionCV given its database id.

Parameters:
pm - the persistence manager
id -
Returns:
Throws:
QueryNotFoundException

findActionApplication

public ActionApplication findActionApplication(javax.jdo.PersistenceManager pm,
                                               long identifier)
                                        throws QueryNotFoundException
Finds a ActionApplication given its database id.

Parameters:
pm - the persistence manager
identifier - the database id of the ActionApplication
Returns:
Throws:
QueryNotFoundException

findSpotLogs

public ActionApplication findSpotLogs(javax.jdo.PersistenceManager pm,
                                      long actionApplicationId)
                               throws QueryNotFoundException
Finds spot logs given an action application database id.

Parameters:
pm - the persistence manager
actionApplicationId -
Returns:
Throws:
QueryNotFoundException

findExperiment

public Experiment findExperiment(javax.jdo.PersistenceManager pm,
                                 java.lang.String name)
                          throws QueryNotFoundException
Finds a Experiment given its name.

Parameters:
pm - the persistence manager
name - the name of the Experiment
Returns:
Throws:
QueryNotFoundException

findExperiment

public Experiment findExperiment(javax.jdo.PersistenceManager pm,
                                 long id)
                          throws QueryNotFoundException
Finds a Experiment given its database id.

Parameters:
pm - the persistence manager
id - the database id of the Experiment
Returns:
Throws:
QueryNotFoundException

findRepeat

public Repeat findRepeat(javax.jdo.PersistenceManager pm,
                         long id)
                  throws QueryNotFoundException
Finds a Repeat given its database id.

Parameters:
pm - the persistence manager
id - the database id of the Repeat
Returns:
Throws:
QueryNotFoundException

findRepeats

protected java.util.Collection<Repeat> findRepeats(javax.jdo.PersistenceManager pm,
                                                   long id)
                                            throws QueryNotFoundException
Gets all repeats for a given experiment using experiment id as an identifier.

Parameters:
pm - the persistence manager
id - Experiments id.
Returns:
collection of repeats which refer to the experiment's id.
Throws:
QueryNotFoundException

findRepeats

protected java.util.Collection<Repeat> findRepeats(javax.jdo.PersistenceManager pm,
                                                   Experiment exp)
                                            throws QueryNotFoundException
Gets all repeats for a given experiment using experiment id as an identifier.

Parameters:
pm - the persistence manager
exp - Experiment to get the repeats of.
Returns:
collection of repeats which refer to the experiment given.
Throws:
QueryNotFoundException

findInoculation

public Inoculation findInoculation(javax.jdo.PersistenceManager pm,
                                   java.lang.Long sourcePlatePosition,
                                   java.lang.Long destinationPlatePosition)
                            throws QueryNotFoundException
Finds a Inoculation given its source and destination PlatePosition DB ids.

Parameters:
pm - the persistence manager
sourcePlatePosition -
destinationPlatePosition -
Returns:
Throws:
QueryNotFoundException

findInoculationWithDestination

public java.util.Collection<Inoculation> findInoculationWithDestination(javax.jdo.PersistenceManager pm,
                                                                        java.lang.Long destinationPlatePosition)
                                                                 throws QueryNotFoundException
Finds a collection of Inoculations given their destination PlatePosition ids.

Parameters:
pm - the persistence manager
destinationPlatePosition -
Returns:
Throws:
QueryNotFoundException

findSpotting

public Spotting findSpotting(javax.jdo.PersistenceManager pm,
                             java.lang.Long sourcePlatePosition,
                             java.lang.Long destinationPlatePosition)
                      throws QueryNotFoundException
Finds a Spotting given its source and destination PlatePosition DB ids.

Parameters:
pm - the persistence manager
sourcePlatePosition - the of the Spotting
destinationPlatePosition - the of the Spotting
Returns:
Throws:
QueryNotFoundException

findSpottingWithDestination

public java.util.Collection<Spotting> findSpottingWithDestination(javax.jdo.PersistenceManager pm,
                                                                  java.lang.Long destinationPlatePosition)
                                                           throws QueryNotFoundException
Finds a collection of Spottings given their destination PlatePosition DB id.

Parameters:
pm - the persistence manager
destinationPlatePosition - the of the Spottings
Returns:
Throws:
QueryNotFoundException

findImageSpot

public java.util.Collection<ImageSpot> findImageSpot(javax.jdo.PersistenceManager pm,
                                                     java.lang.Long sourcePlatePosition)
                                              throws QueryNotFoundException
Finds a ImageSpot given its source PlatePosition database id.

Parameters:
pm - the persistence manager
sourcePlatePosition - the database id of the source plate position
Returns:
Throws:
QueryNotFoundException

findPosition

public Position findPosition(javax.jdo.PersistenceManager pm,
                             int row,
                             int column)
                      throws QueryNotFoundException
Finds a Position given its row and column.

Parameters:
pm - the persistence manager
row -
column -
Returns:
Throws:
QueryNotFoundException

findPlatePosition

public PlatePosition findPlatePosition(javax.jdo.PersistenceManager pm,
                                       java.lang.String barcode,
                                       java.lang.Long positionId)
                                throws QueryNotFoundException
Finds a PlatePosition given its Barcode value and Position DB id.

Parameters:
pm - the persistence manager
barcode -
positionId -
Returns:
Throws:
QueryNotFoundException

findPlatePosition

public PlatePosition findPlatePosition(javax.jdo.PersistenceManager pm,
                                       java.lang.String barcode,
                                       int row,
                                       int column)
                                throws QueryNotFoundException
Finds a PlatePosition given its Barcode value and row and column position.

Parameters:
pm - the persistence manager
barcode - the barcode of the plate
row - the row of the position
column - the column of the position
Returns:
Throws:
QueryNotFoundException

findPlatePosition

public PlatePosition findPlatePosition(javax.jdo.PersistenceManager pm,
                                       java.lang.Long barcodeId,
                                       java.lang.Long positionId)
                                throws QueryNotFoundException
Finds a PlatePosition given its Barcode and Position DB ids.

Parameters:
pm - the persistence manager
barcodeId - the of the PlatePosition
positionId - the of the PlatePosition
Returns:
Throws:
QueryNotFoundException

findPlatePosition

public PlatePosition findPlatePosition(javax.jdo.PersistenceManager pm,
                                       java.lang.Long id)
                                throws QueryNotFoundException
Finds a PlatePosition given its DB id.

Parameters:
pm - the persistence manager
id -
Returns:
Throws:
QueryNotFoundException

forceFindPosition

public Position forceFindPosition(javax.jdo.PersistenceManager pm,
                                  int row,
                                  int column)
Finds a Position given its row and column.

Parameters:
pm - the persistence manager
row -
column -
Returns:

forceFindPlatePosition

public PlatePosition forceFindPlatePosition(javax.jdo.PersistenceManager pm,
                                            long barcodeId,
                                            int row,
                                            int column)
                                     throws QueryNotFoundException
Finds or creates a PlatePosition given its Barcode DB id and row and column.

Parameters:
pm - the persistence manager
barcodeId - the of the PlatePosition
row - the of the PlatePosition
column - the of the PlatePosition
Returns:
Throws:
QueryNotFoundException

forceFindPlatePosition

public PlatePosition forceFindPlatePosition(javax.jdo.PersistenceManager pm,
                                            java.lang.String barcode,
                                            int row,
                                            int column)
                                     throws QueryNotFoundException
Finds or creates a PlatePosition given its Barcode value and row and column .

Parameters:
pm - the persistence manager
barcode - the of the PlatePosition
row - the of the PlatePosition
column - the of the PlatePosition
Returns:
Throws:
QueryNotFoundException

fillPlateList

public java.util.Map<java.lang.String,java.lang.Exception> fillPlateList(javax.jdo.PersistenceManager pm,
                                                                         java.util.List<java.lang.String> barcodes,
                                                                         java.util.List<Plate> listToFill)
Fills the given list using the given barcodes with Plates from the DB.

Parameters:
pm - the persistence manager
barcodes - the barcodes of the plates
listToFill - the list to fill with Plates
Returns:


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