gov.nih.nci.caarray.services.experiment
Class ExperimentManagerDB

java.lang.Object
  extended by gov.nih.nci.caarray.services.util.db.ManagerDB
      extended by gov.nih.nci.caarray.services.experiment.ExperimentManagerDB

public final class ExperimentManagerDB
extends ManagerDB

Author:
TranP

Field Summary
 
Fields inherited from class gov.nih.nci.caarray.services.util.db.ManagerDB
CASCADE_LINK, CASCADE_NONE, CASCADE_OBJECT, ID_UNSET
 
Constructor Summary
ExperimentManagerDB()
           
 
Method Summary
 long addAdditionalDataProcessing(long experimentId, AdditionalDataProcessing additionalProcessing)
           
 long addAdditionalQualifier(long experimentId, OntologyEntry qualifier)
           
 long addAdditionalUploadedFile(long experimentId, AdditionalUploadedFile additionalUploadedFile)
           
 long addBibliographicReference(long experimentId, BibliographicReference bf)
           
 long addExperiment(Experiment experiment)
          Add the specified Experiment to the persistence store
 long addExperimentalFactor(long experimentId, ExperimentalFactor factor)
           
 void addExperimentalFactors(long experimentId, ExperimentalFactor[] factors)
           
 long addFactorValue(long experimentalFactorId, FactorValue value)
           
 void addFactorValues(long experimentalFactorId, FactorValue[] values)
           
 long addHybridizationFileUpload(long experimentId, HybridizationFileUpload hybUpload)
          This method performs the following: Add caARRAY-specific HybridizationFileUpload to the persistence store.
 long[] addHybridizationFileUploads(long experimentId, HybridizationFileUpload[] hybUploads)
           
 long addQualityControl(long experimentId, Description qualityControl)
           
 void close()
          Close database connection.
 void convertFactorValueMeasurementsToValues(Experiment exp)
           
 int countHybridizationFileUploadEntries(long experimentId)
           
 int countHybridizationFileUploads(long experimentId)
          Deprecated. This method was replaced by countHybridizationFileUploadEntries for the redesigned
 void deleteAdditionalDataProcessing(long experimentId, long additionalDataProcessingId)
           
 void deleteAdditionalQualifier(long experimentId, long qualifierId)
           
 void deleteAdditionalUploadedFile(long experimentId, long additionalUploadedFileId)
           
 void deleteBibliographicReferenceFromExperiment(long experimentId, long bfId)
           
 boolean deleteBioAssayFromExperiment(BioAssay bioAssay, Experiment experiment)
           
 void deleteExperiment(long experimentId)
           
 void deleteExperimentalFactorFromExperiment(long experimentId, long factorId)
           
 void deleteFactorValueFromExperimentalFactor(long experimentalFactorId, long valueId)
           
 void deleteHybridizationFileUploadEntryFromExperiment(long experimentId, long id)
           
 void deleteHybridizationFileUploadFromExperiment(long experimentId, long id)
           
 void deleteQualityControlFromExperiment(long experimentId, long qualityControlId)
           
 AdditionalDataProcessing getAdditionalDataProcessing(long addDataProcessingId)
           
 AdditionalDataProcessing[] getAdditionalDataProcessings(long experimentId)
           
 OntologyEntry getAdditionalQualifier(long id)
           
 AdditionalUploadedFile getAdditionalUploadedFile(long uploadedFileId)
           
 AdditionalUploadedFile[] getAdditionalUploadedFiles(long experimentId)
           
 Array getArray(long id)
          This method returns a Array that has the specified ID by delegating the call to the same method in ArrayManagerDB.
 PhysicalArrayDesign getArrayDesign(long id)
          This method returns a PhysicalArrayDesign that has the specified ID by delegating the call to the same method in ArrayDesignManagerDB.
 BibliographicReference getBibliographicReference(long id)
           
 Experiment getExperiment(long id)
           
 ExperimentalFactor getExperimentalFactor(long id)
           
 ExperimentalFactor[] getExperimentalFactors(long experimentId)
           
 java.util.Date getExperimentDate(long experimentId)
          Workaround for efficiency to get the date for experiment fast.
 Experiment[] getExperiments(ExperimentSearchCriteria criteria)
          Gets Experiments.
 Experiment[] getExperimentsReferencingArrayGroup(long arrayGroupId)
           
 FactorValue[] getFactorValues(long experimentalFactorId)
           
 HybridizationFileUpload getHybridizationFileUpload(long hybUploadId)
           
 HybridizationFileUpload[] getHybridizationFileUploads(long experimentId)
           
 HybridizationFileUpload[] getHybridizationFileUploads(long[] hybUploadIds)
           
 Protocol getProtocol(long id)
          This method returns a Protocol that has the specified ID by delegating the call to the same method in ProtocolManagerDB.
 Description getQualityControlDescription(long id)
           
 void updateAdditionalQualifier(OntologyEntry qualifier)
           
 void updateBibliographicReference(BibliographicReference bf)
           
 void updateExperiment(Experiment experiment)
           
 void updateExperimentalFactor(ExperimentalFactor factor)
           
 void updateHybridizationFileUpload(HybridizationFileUpload hybUpload)
           
 void updateProtocolApplication(ProtocolApplicationData paData)
           
 void updateQualityControl(Description qualityControl)
           
 
Methods inherited from class gov.nih.nci.caarray.services.util.db.ManagerDB
clearCache, countObjects, countObjects, deleteByQuery, deleteMtoNRelation, deleteObject, deleteObject, deleteObject, deleteObjectByQuery, exists, getIdentifiable, getObject, getObject, getObject, getObject, getObject, getObject, getObjectIterator, getObjectIterator, getObjects, getObjects, getObjects, getPersistenceBroker, getSqlInLimit, insertMtoNRelation, insertMtoNRelation, insertObject, insertObject, link, link, removeFromCache, retrieveReference, retrieveReferences, setCascadeDelete, setCascadeRetrieve, setCascadeStore, storeObject, storeObject, unlink, unlink, updateObject, updateObject
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ExperimentManagerDB

public ExperimentManagerDB()
Method Detail

getExperiment

public Experiment getExperiment(long id)
                         throws java.lang.Exception
Parameters:
id -
Returns:
Throws:
ObjectNotExistException
DBException
java.lang.Exception

addExperiment

public long addExperiment(Experiment experiment)
                   throws java.lang.Exception
Add the specified Experiment to the persistence store

Returns:
- An object representing the ID of the Experiment being inserted or null otherwise.
Throws:
java.lang.Exception

updateExperiment

public void updateExperiment(Experiment experiment)
                      throws java.lang.Exception
Throws:
java.lang.Exception

getBibliographicReference

public BibliographicReference getBibliographicReference(long id)
                                                 throws java.lang.Exception
Throws:
java.lang.Exception

addBibliographicReference

public long addBibliographicReference(long experimentId,
                                      BibliographicReference bf)
                               throws java.lang.Exception
Throws:
java.lang.Exception

updateBibliographicReference

public void updateBibliographicReference(BibliographicReference bf)
                                  throws java.lang.Exception
Throws:
java.lang.Exception

deleteBibliographicReferenceFromExperiment

public void deleteBibliographicReferenceFromExperiment(long experimentId,
                                                       long bfId)
                                                throws java.lang.Exception
Parameters:
id -
Throws:
ObjectNotExistException
DBException
java.lang.Exception

addAdditionalQualifier

public long addAdditionalQualifier(long experimentId,
                                   OntologyEntry qualifier)
                            throws java.lang.Exception
Parameters:
experimentId -
qualifier -
Throws:
ObjectNotExistException
InsertObjectException
DBException
java.lang.Exception

updateAdditionalQualifier

public void updateAdditionalQualifier(OntologyEntry qualifier)
                               throws java.lang.Exception
Parameters:
qualifier -
Throws:
ObjectNotExistException
DBException
java.lang.Exception

addExperimentalFactor

public long addExperimentalFactor(long experimentId,
                                  ExperimentalFactor factor)
                           throws java.lang.Exception
Throws:
java.lang.Exception

addExperimentalFactors

public void addExperimentalFactors(long experimentId,
                                   ExperimentalFactor[] factors)
                            throws java.lang.Exception
Throws:
java.lang.Exception

addFactorValue

public long addFactorValue(long experimentalFactorId,
                           FactorValue value)
                    throws java.lang.Exception
Throws:
java.lang.Exception

addFactorValues

public void addFactorValues(long experimentalFactorId,
                            FactorValue[] values)
                     throws java.lang.Exception
Throws:
java.lang.Exception

convertFactorValueMeasurementsToValues

public void convertFactorValueMeasurementsToValues(Experiment exp)

getFactorValues

public FactorValue[] getFactorValues(long experimentalFactorId)
                              throws java.lang.Exception
Throws:
java.lang.Exception

updateProtocolApplication

public void updateProtocolApplication(ProtocolApplicationData paData)
                               throws java.lang.Exception
Throws:
java.lang.Exception

deleteFactorValueFromExperimentalFactor

public void deleteFactorValueFromExperimentalFactor(long experimentalFactorId,
                                                    long valueId)
                                             throws java.lang.Exception
Throws:
java.lang.Exception

getAdditionalQualifier

public OntologyEntry getAdditionalQualifier(long id)
                                     throws java.lang.Exception
Throws:
java.lang.Exception

getExperimentalFactor

public ExperimentalFactor getExperimentalFactor(long id)
                                         throws java.lang.Exception
Throws:
java.lang.Exception

getExperimentalFactors

public ExperimentalFactor[] getExperimentalFactors(long experimentId)
                                            throws java.lang.Exception
Throws:
java.lang.Exception

updateExperimentalFactor

public void updateExperimentalFactor(ExperimentalFactor factor)
                              throws java.lang.Exception
Throws:
java.lang.Exception

deleteExperimentalFactorFromExperiment

public void deleteExperimentalFactorFromExperiment(long experimentId,
                                                   long factorId)
                                            throws java.lang.Exception
Parameters:
experimentId -
factorId -
Throws:
ObjectNotExistException
DBException
java.lang.Exception

deleteExperiment

public void deleteExperiment(long experimentId)
                      throws java.lang.Exception
Parameters:
id -
Throws:
ObjectNotExistException
DBException
java.lang.Exception

deleteAdditionalQualifier

public void deleteAdditionalQualifier(long experimentId,
                                      long qualifierId)
                               throws java.lang.Exception
Parameters:
id -
Throws:
ObjectNotExistException
DBException
java.lang.Exception

getExperiments

public Experiment[] getExperiments(ExperimentSearchCriteria criteria)
Gets Experiments.

Returns:

getQualityControlDescription

public Description getQualityControlDescription(long id)
                                         throws java.lang.Exception
Throws:
java.lang.Exception

addQualityControl

public long addQualityControl(long experimentId,
                              Description qualityControl)
                       throws java.lang.Exception
Throws:
java.lang.Exception

updateQualityControl

public void updateQualityControl(Description qualityControl)
                          throws java.lang.Exception
Throws:
java.lang.Exception

deleteQualityControlFromExperiment

public void deleteQualityControlFromExperiment(long experimentId,
                                               long qualityControlId)
                                        throws java.lang.Exception
Parameters:
id -
Throws:
ObjectNotExistException
DBException
java.lang.Exception

addAdditionalDataProcessing

public long addAdditionalDataProcessing(long experimentId,
                                        AdditionalDataProcessing additionalProcessing)
                                 throws java.lang.Exception
Throws:
java.lang.Exception

addAdditionalUploadedFile

public long addAdditionalUploadedFile(long experimentId,
                                      AdditionalUploadedFile additionalUploadedFile)
                               throws java.lang.Exception
Throws:
java.lang.Exception

deleteAdditionalDataProcessing

public void deleteAdditionalDataProcessing(long experimentId,
                                           long additionalDataProcessingId)
                                    throws java.lang.Exception
Throws:
java.lang.Exception

deleteAdditionalUploadedFile

public void deleteAdditionalUploadedFile(long experimentId,
                                         long additionalUploadedFileId)
                                  throws java.lang.Exception
Throws:
java.lang.Exception

getAdditionalDataProcessing

public AdditionalDataProcessing getAdditionalDataProcessing(long addDataProcessingId)
                                                     throws java.lang.Exception
Throws:
java.lang.Exception

getAdditionalDataProcessings

public AdditionalDataProcessing[] getAdditionalDataProcessings(long experimentId)
                                                        throws java.lang.Exception
Throws:
java.lang.Exception

getAdditionalUploadedFile

public AdditionalUploadedFile getAdditionalUploadedFile(long uploadedFileId)
                                                 throws java.lang.Exception
Throws:
java.lang.Exception

getAdditionalUploadedFiles

public AdditionalUploadedFile[] getAdditionalUploadedFiles(long experimentId)
                                                    throws java.lang.Exception
Throws:
java.lang.Exception

getHybridizationFileUpload

public HybridizationFileUpload getHybridizationFileUpload(long hybUploadId)
                                                   throws java.lang.Exception
Throws:
java.lang.Exception

getHybridizationFileUploads

public HybridizationFileUpload[] getHybridizationFileUploads(long[] hybUploadIds)
                                                      throws java.lang.Exception
Throws:
java.lang.Exception

countHybridizationFileUploads

public int countHybridizationFileUploads(long experimentId)
                                  throws java.lang.Exception
Deprecated. This method was replaced by countHybridizationFileUploadEntries for the redesigned

Parameters:
experimentId -
Returns:
Throws:
DBException
java.lang.Exception

countHybridizationFileUploadEntries

public int countHybridizationFileUploadEntries(long experimentId)
                                        throws java.lang.Exception
Throws:
java.lang.Exception

getExperimentDate

public java.util.Date getExperimentDate(long experimentId)
                                 throws java.lang.Exception
Workaround for efficiency to get the date for experiment fast.

Throws:
java.lang.Exception

getHybridizationFileUploads

public HybridizationFileUpload[] getHybridizationFileUploads(long experimentId)
                                                      throws java.lang.Exception
Throws:
java.lang.Exception

addHybridizationFileUpload

public long addHybridizationFileUpload(long experimentId,
                                       HybridizationFileUpload hybUpload)
                                throws java.lang.Exception
This method performs the following:

Parameters:
experimentId -
upload -
Returns:
Throws:
ObjectNotExistException
InsertObjectException
DBException
java.lang.Exception

addHybridizationFileUploads

public long[] addHybridizationFileUploads(long experimentId,
                                          HybridizationFileUpload[] hybUploads)
                                   throws java.lang.Exception
Throws:
java.lang.Exception

updateHybridizationFileUpload

public void updateHybridizationFileUpload(HybridizationFileUpload hybUpload)
                                   throws java.lang.Exception
Throws:
java.lang.Exception

deleteHybridizationFileUploadFromExperiment

public void deleteHybridizationFileUploadFromExperiment(long experimentId,
                                                        long id)
                                                 throws java.lang.Exception
Throws:
java.lang.Exception

deleteHybridizationFileUploadEntryFromExperiment

public void deleteHybridizationFileUploadEntryFromExperiment(long experimentId,
                                                             long id)
                                                      throws java.lang.Exception
Throws:
java.lang.Exception

getProtocol

public Protocol getProtocol(long id)
                     throws java.lang.Exception
This method returns a Protocol that has the specified ID by delegating the call to the same method in ProtocolManagerDB. This allows ExperimentManagerEJB to interface with a single ManagerDB.

Parameters:
id -
Returns:
Throws:
java.lang.Exception

getArrayDesign

public PhysicalArrayDesign getArrayDesign(long id)
                                   throws java.lang.Exception
This method returns a PhysicalArrayDesign that has the specified ID by delegating the call to the same method in ArrayDesignManagerDB. This allows ExperimentManagerEJB to interface with a single ManagerDB.

Parameters:
id -
Returns:
Throws:
java.lang.Exception

getArray

public Array getArray(long id)
               throws java.lang.Exception
This method returns a Array that has the specified ID by delegating the call to the same method in ArrayManagerDB.

Parameters:
id -
Returns:
Throws:
java.lang.Exception

getExperimentsReferencingArrayGroup

public Experiment[] getExperimentsReferencingArrayGroup(long arrayGroupId)
                                                 throws java.lang.Exception
Throws:
java.lang.Exception

deleteBioAssayFromExperiment

public boolean deleteBioAssayFromExperiment(BioAssay bioAssay,
                                            Experiment experiment)
                                     throws java.lang.Exception
Throws:
java.lang.Exception

close

public void close()
Description copied from class: ManagerDB
Close database connection.

Overrides:
close in class ManagerDB