gov.nih.nci.caarray.common.delegate
Class BioMaterialManagerDelegate

java.lang.Object
  extended by gov.nih.nci.caarray.common.delegate.BioMaterialManagerDelegate

public final class BioMaterialManagerDelegate
extends java.lang.Object

Author:
TranP, matyass

Constructor Summary
BioMaterialManagerDelegate()
           
 
Method Summary
 long addBioSample(BioSampleData bioSampleData)
           
 long addBioSource(BioSourceData bioSourceData, VocabData[] characteristics)
           
 long addTreatmentToBioSample(long bioSampleId, TreatmentData treatmentData)
           
 long addTreatmentToLabeledExtract(long labeledExtractId, TreatmentData treatmentData)
           
 long copyLabeledExtract(long labeledExtractId, java.lang.String newLabeledExtractName)
           
 void deleteBioSample(long bioMaterialId)
           
 void deleteBioSource(long bioMaterialId)
           
 void deleteLabeledExtract(long bioMaterialId)
           
 void deleteTreatmentFromBioMaterial(long bioMaterialId, long treatmentId)
           
 long duplicateBioSource(long sourceBioSourceId, java.lang.String dupBiosourceName)
           
 long duplicateLabelExtract(long sourceLabelExtractId, java.lang.String dupLabelExtractName)
           
 BioMaterialData getBioMaterial(long id)
           
 BioSampleData getBioSample(long id)
           
 BioSampleView getBioSampleView(long id)
           
 BioSourceData getBioSource(long id)
           
 BioSourceView getBioSourceView(long id)
           
 LabeledExtractData getLabeledExtract(long id)
           
 LabeledExtractView getLabeledExtractView(long id)
           
 TreatmentData getTreatment(long id)
           
 TreatmentData[] getTreatments(long bioMaterialId)
           
 long labelBioSample(TreatmentData labelingTreatment, LabeledExtractData extractData)
           
 long poolBioSamples(TreatmentData poolingTreatment, BioSampleData outputBioSample)
           
 BioMaterialDesc[] searchBioMaterials(BioMaterialSearchCriteria criteria)
          Deprecated. No uses appear to be found, possible dead code
 BioSampleDesc[] searchBioSamples(BioMaterialSearchCriteria criteria)
           
 BioSampleDesc[] searchBioSamples(BioMaterialSearchCriteria criteria, boolean ownerOnly)
          deprecated No uses appear to be found, possible dead code
 BioSampleDesc[] searchBioSamples(BioMaterialSearchCriteria criteria, int pageSize, int pageNum)
           
 BioSampleDesc[] searchBioSamplesShallow(BioMaterialSearchCriteria criteria)
          Perform a shallow search (used typically to populate pull-down lists in UI)
 BioSampleDesc[] searchBioSamplesShallow(BioMaterialSearchCriteria criteria, boolean ownerOnly)
          Perform a shallow search (used typically to populate pull-down lists in UI)
 BioSourceDesc[] searchBioSources(BioMaterialSearchCriteria criteria)
           
 BioSourceDesc[] searchBioSources(BioMaterialSearchCriteria criteria, boolean ownerOnly)
          Deprecated. No uses appear to be found, possible dead code
 BioSourceDesc[] searchBioSources(BioMaterialSearchCriteria criteria, int pageSize, int pageNum)
           
 BioSourceDesc[] searchBioSourcesShallow(BioMaterialSearchCriteria criteria)
          Perform a shallow search (used typically to populate pull-down lists in UI)
 BioSourceDesc[] searchBioSourcesShallow(BioMaterialSearchCriteria criteria, boolean ownerOnly)
          Perform a shallow search (used typically to populate pull-down lists in UI)
 LabeledExtractDesc[] searchLabeledExtracts(BioMaterialSearchCriteria criteria)
           
 LabeledExtractDesc[] searchLabeledExtracts(BioMaterialSearchCriteria criteria, int pageSize, int pageNum)
           
 LabeledExtractDesc[] searchLabeledExtractsShallow(BioMaterialSearchCriteria criteria)
           
 long[] splitBioSample(TreatmentData splittingTreatment, SplitBioSampleData[] outputBioSamples)
           
 long treatBioMaterial(TreatmentData[] treatmentData, BioMaterialData outputBioMaterialData)
           
 long treatBioMaterial(TreatmentData treatmentData, BioMaterialData outputBioMaterialData)
           
 void updateBioMaterialCharacteristics(long bioMaterialId, VocabData[] characteristics)
           
 void updateBioSample(BioSampleData bioSampleData)
           
 void updateBioSource(BioSourceData bioSourceData)
           
 void updateLabeledExtract(TreatmentData labelingTreatment, LabeledExtractData extractData)
           
 void updateTreatment(TreatmentData treatmentData)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BioMaterialManagerDelegate

public BioMaterialManagerDelegate()
Method Detail

addBioSample

public long addBioSample(BioSampleData bioSampleData)
                  throws java.lang.Exception
Throws:
java.lang.Exception

addBioSource

public long addBioSource(BioSourceData bioSourceData,
                         VocabData[] characteristics)
                  throws java.lang.Exception
Throws:
java.lang.Exception

deleteTreatmentFromBioMaterial

public void deleteTreatmentFromBioMaterial(long bioMaterialId,
                                           long treatmentId)
                                    throws java.lang.Exception
Throws:
java.lang.Exception

deleteBioSample

public void deleteBioSample(long bioMaterialId)
                     throws java.lang.Exception
Throws:
java.lang.Exception

deleteBioSource

public void deleteBioSource(long bioMaterialId)
                     throws java.lang.Exception
Throws:
java.lang.Exception

deleteLabeledExtract

public void deleteLabeledExtract(long bioMaterialId)
                          throws java.lang.Exception
Throws:
java.lang.Exception

duplicateBioSource

public long duplicateBioSource(long sourceBioSourceId,
                               java.lang.String dupBiosourceName)
                        throws java.lang.Exception
Throws:
java.lang.Exception

duplicateLabelExtract

public long duplicateLabelExtract(long sourceLabelExtractId,
                                  java.lang.String dupLabelExtractName)
                           throws java.lang.Exception
Throws:
java.lang.Exception

getBioSample

public BioSampleData getBioSample(long id)
                           throws java.lang.Exception
Throws:
java.lang.Exception

getTreatment

public TreatmentData getTreatment(long id)
                           throws java.lang.Exception
Throws:
java.lang.Exception

getBioSampleView

public BioSampleView getBioSampleView(long id)
                               throws java.lang.Exception
Throws:
java.lang.Exception

getBioMaterial

public BioMaterialData getBioMaterial(long id)
                               throws java.lang.Exception
Throws:
java.lang.Exception

getBioSource

public BioSourceData getBioSource(long id)
                           throws java.lang.Exception
Throws:
java.lang.Exception

getBioSourceView

public BioSourceView getBioSourceView(long id)
                               throws java.lang.Exception
Parameters:
id -
Returns:
Throws:
AccessDeniedException
ObjectNotExistException
GeneralException
java.lang.Exception

getLabeledExtract

public LabeledExtractData getLabeledExtract(long id)
                                     throws java.lang.Exception
Throws:
java.lang.Exception

getLabeledExtractView

public LabeledExtractView getLabeledExtractView(long id)
                                         throws java.lang.Exception
Throws:
java.lang.Exception

labelBioSample

public long labelBioSample(TreatmentData labelingTreatment,
                           LabeledExtractData extractData)
                    throws java.lang.Exception
Throws:
java.lang.Exception

poolBioSamples

public long poolBioSamples(TreatmentData poolingTreatment,
                           BioSampleData outputBioSample)
                    throws java.lang.Exception
Throws:
java.lang.Exception

searchBioMaterials

public BioMaterialDesc[] searchBioMaterials(BioMaterialSearchCriteria criteria)
                                     throws java.lang.Exception
Deprecated. No uses appear to be found, possible dead code

Throws:
java.lang.Exception

searchBioSamplesShallow

public BioSampleDesc[] searchBioSamplesShallow(BioMaterialSearchCriteria criteria)
                                        throws java.lang.Exception
Perform a shallow search (used typically to populate pull-down lists in UI)

Throws:
java.lang.Exception

searchBioSamplesShallow

public BioSampleDesc[] searchBioSamplesShallow(BioMaterialSearchCriteria criteria,
                                               boolean ownerOnly)
                                        throws java.lang.Exception
Perform a shallow search (used typically to populate pull-down lists in UI)

Throws:
java.lang.Exception

searchBioSamples

public BioSampleDesc[] searchBioSamples(BioMaterialSearchCriteria criteria)
                                 throws java.lang.Exception
Throws:
java.lang.Exception

searchBioSamples

public BioSampleDesc[] searchBioSamples(BioMaterialSearchCriteria criteria,
                                        boolean ownerOnly)
                                 throws java.lang.Exception
deprecated No uses appear to be found, possible dead code

Throws:
java.lang.Exception

searchBioSamples

public BioSampleDesc[] searchBioSamples(BioMaterialSearchCriteria criteria,
                                        int pageSize,
                                        int pageNum)
                                 throws java.lang.Exception
Throws:
java.lang.Exception

searchBioSources

public BioSourceDesc[] searchBioSources(BioMaterialSearchCriteria criteria)
                                 throws java.lang.Exception
Throws:
java.lang.Exception

searchBioSourcesShallow

public BioSourceDesc[] searchBioSourcesShallow(BioMaterialSearchCriteria criteria)
                                        throws java.lang.Exception
Perform a shallow search (used typically to populate pull-down lists in UI)

Throws:
java.lang.Exception

searchBioSourcesShallow

public BioSourceDesc[] searchBioSourcesShallow(BioMaterialSearchCriteria criteria,
                                               boolean ownerOnly)
                                        throws java.lang.Exception
Perform a shallow search (used typically to populate pull-down lists in UI)

Throws:
java.lang.Exception

searchBioSources

public BioSourceDesc[] searchBioSources(BioMaterialSearchCriteria criteria,
                                        boolean ownerOnly)
                                 throws java.lang.Exception
Deprecated. No uses appear to be found, possible dead code

Throws:
java.lang.Exception

searchBioSources

public BioSourceDesc[] searchBioSources(BioMaterialSearchCriteria criteria,
                                        int pageSize,
                                        int pageNum)
                                 throws java.lang.Exception
Throws:
java.lang.Exception

searchLabeledExtracts

public LabeledExtractDesc[] searchLabeledExtracts(BioMaterialSearchCriteria criteria)
                                           throws java.lang.Exception
Throws:
java.lang.Exception

searchLabeledExtractsShallow

public LabeledExtractDesc[] searchLabeledExtractsShallow(BioMaterialSearchCriteria criteria)
                                                  throws java.lang.Exception
Throws:
java.lang.Exception

searchLabeledExtracts

public LabeledExtractDesc[] searchLabeledExtracts(BioMaterialSearchCriteria criteria,
                                                  int pageSize,
                                                  int pageNum)
                                           throws java.lang.Exception
Throws:
java.lang.Exception

splitBioSample

public long[] splitBioSample(TreatmentData splittingTreatment,
                             SplitBioSampleData[] outputBioSamples)
                      throws java.lang.Exception
Throws:
java.lang.Exception

getTreatments

public TreatmentData[] getTreatments(long bioMaterialId)
                              throws java.lang.Exception
Throws:
java.lang.Exception

treatBioMaterial

public long treatBioMaterial(TreatmentData treatmentData,
                             BioMaterialData outputBioMaterialData)
                      throws java.lang.Exception
Throws:
java.lang.Exception

treatBioMaterial

public long treatBioMaterial(TreatmentData[] treatmentData,
                             BioMaterialData outputBioMaterialData)
                      throws java.lang.Exception
Throws:
java.lang.Exception

updateBioMaterialCharacteristics

public void updateBioMaterialCharacteristics(long bioMaterialId,
                                             VocabData[] characteristics)
                                      throws java.lang.Exception
Throws:
java.lang.Exception

updateBioSample

public void updateBioSample(BioSampleData bioSampleData)
                     throws java.lang.Exception
Throws:
java.lang.Exception

updateTreatment

public void updateTreatment(TreatmentData treatmentData)
                     throws java.lang.Exception
Parameters:
treatmentData -
Throws:
AccessDeniedException
ObjectNotExistException
GeneralException
java.lang.Exception

updateBioSource

public void updateBioSource(BioSourceData bioSourceData)
                     throws java.lang.Exception
Throws:
java.lang.Exception

updateLabeledExtract

public void updateLabeledExtract(TreatmentData labelingTreatment,
                                 LabeledExtractData extractData)
                          throws java.lang.Exception
Throws:
java.lang.Exception

addTreatmentToBioSample

public long addTreatmentToBioSample(long bioSampleId,
                                    TreatmentData treatmentData)
                             throws java.lang.Exception
Parameters:
bioSampleId -
treatmentData -
Returns:
Throws:
AccessDeniedException
ObjectNotExistException
InsertObjectException
GeneralException
java.lang.Exception

addTreatmentToLabeledExtract

public long addTreatmentToLabeledExtract(long labeledExtractId,
                                         TreatmentData treatmentData)
                                  throws java.lang.Exception
Throws:
java.lang.Exception

copyLabeledExtract

public long copyLabeledExtract(long labeledExtractId,
                               java.lang.String newLabeledExtractName)
                        throws java.lang.Exception
Throws:
java.lang.Exception