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

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

public final class ExperimentManagerDelegate
extends java.lang.Object

Author:
Tranp

Constructor Summary
ExperimentManagerDelegate()
           
 
Method Summary
 void addAdditionalDataProcessing(long expId, AdditionalDataProcessingData data)
           
 void addAdditionalQualifier(long expId, AdditionalQualifierData addQualifier)
           
 void addAdditionalUploadedFile(long expId, AdditionalUploadedFileData data)
           
 long addExperiment(ExperimentData experiment)
           
 long addExperiment(ExperimentData experiment, ExperimentalFactorData[] factors)
           
 void addExperimentalFactors(long expId, ExperimentalFactorData[] expFactor)
           
 long addFactorValue(long experimentalFactorId, FactorValueData valueData)
           
 long addHybridizationFileUpload(long expId, HybridizationFileUploadData hybData)
           
 HybridizationFileUploadData[] addHybridizationFileUploads(long experimentId, HybridizationFileUploadData[] uploadData)
           
 void addPublication(long expId, PublicationData pubData)
           
 void addQualityControl(long expId, QualityControlData qualityControl)
           
 boolean checkBatchDownloadFile(long experimentId, java.lang.String fileType)
           
 void deleteAdditionalDataProcessingFromExperiment(long expId, long dataId)
           
 void deleteAdditionalQualifierFromExperiment(long expId, long qualifierId)
           
 void deleteAdditionalUploadedFileFromExperiment(long expId, long fileId)
           
 ExperimentDeletionResult deleteExperiment(ExperimentData experimentData)
           
 void deleteExperiment(long expId)
           
 void deleteExperimentalFactorFromExperiment(long expId, long factorId)
           
 void deleteFactorValueFromExperimentalFactor(long experimentalFactorId, long factorValueId)
           
 void deleteHybridizationFileUploadFromExperiment(long experimentId, long id)
           
 HybridizationDeletionResult deleteHybridizations(HybridizationDeletionConfiguration configuration)
           
 void deletePublicationFromExperiment(long experimentId, long publicationId)
           
 void deleteQualityControlFromExperiment(long expId, long qualityId)
           
 AdditionalDataProcessingData getAdditionalDataProcessing(long id)
           
 AdditionalUploadedFileData getAdditionalUploadedFile(long id)
           
 java.lang.String getDataFilesDirectory(long experimentId)
           
 ExperimentData getExperiment(long expId)
           
 ExperimentView getExperimentView(long expId)
           
 FactorValueData[] getFactorValues(long experimentalFactorId)
           
 HybridizationFileUploadData getHybridizationFileUpload(long hybUploadId)
           
 HybridizationFileUploadData[] getHybridizationFileUploads(long expId)
           
 HybridizationFileUploadData[] getHybridizationFileUploads(long[] hybIds)
           
 java.lang.String getInputFilesDirectory()
           
 java.lang.String getInputFilesDirectory(long experimentId)
          Use to get directory for download files.
 FileData getLatestMAGEML(long experimentId)
           
 ExperimentCleaningConfiguration loadInformation(ExperimentCleaningConfiguration configuration)
           
 void lockExperiment(long expId)
           
 ExperimentDesc[] searchExperiments(ExperimentSearchCriteria criteria)
           
 ExperimentDesc[] searchExperiments(ExperimentSearchCriteria criteria, int pageSize, int pageNum)
           
 void submitHybridizationFileUploadsForParsing(long experimentId, long[] hybUploadIds)
           
 void submitMAGEMLFile(java.lang.String magemlFilePathName)
           
 void submitMAGEMLGeneration(long experimentId)
           
 void updateAdditionalQualifier(long expId, AdditionalQualifierData qualifierData)
           
 void updateExperiment(ExperimentData expData)
           
 void updateExperimentalFactor(long experimentId, ExperimentalFactorData factor)
           
 void updateExperimentalFactors(long expId, ExperimentalFactorData[] factorData)
           
 void updateHybridizationFileUpload(HybridizationFileUploadData hypUpload)
           
 void updateProtocolApplication(ProtocolApplicationData data)
           
 void updatePublication(long expId, PublicationData pubData)
           
 void updateQualityControl(long expId, QualityControlData qualityControl)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ExperimentManagerDelegate

public ExperimentManagerDelegate()
Method Detail

addExperiment

public long addExperiment(ExperimentData experiment,
                          ExperimentalFactorData[] factors)
                   throws java.lang.Exception
Throws:
java.lang.Exception

addExperiment

public long addExperiment(ExperimentData experiment)
                   throws java.lang.Exception
Throws:
java.lang.Exception

addAdditionalQualifier

public void addAdditionalQualifier(long expId,
                                   AdditionalQualifierData addQualifier)
                            throws java.lang.Exception
Throws:
java.lang.Exception

addExperimentalFactors

public void addExperimentalFactors(long expId,
                                   ExperimentalFactorData[] expFactor)
                            throws java.lang.Exception
Throws:
java.lang.Exception

addHybridizationFileUpload

public long addHybridizationFileUpload(long expId,
                                       HybridizationFileUploadData hybData)
                                throws java.lang.Exception
Throws:
java.lang.Exception

addHybridizationFileUploads

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

getHybridizationFileUploads

public HybridizationFileUploadData[] getHybridizationFileUploads(long expId)
                                                          throws java.lang.Exception
Throws:
java.lang.Exception

getHybridizationFileUploads

public HybridizationFileUploadData[] getHybridizationFileUploads(long[] hybIds)
                                                          throws java.lang.Exception
Throws:
java.lang.Exception

updateHybridizationFileUpload

public void updateHybridizationFileUpload(HybridizationFileUploadData hypUpload)
                                   throws java.lang.Exception
Throws:
java.lang.Exception

getHybridizationFileUpload

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

addPublication

public void addPublication(long expId,
                           PublicationData pubData)
                    throws java.lang.Exception
Throws:
java.lang.Exception

addQualityControl

public void addQualityControl(long expId,
                              QualityControlData qualityControl)
                       throws java.lang.Exception
Throws:
java.lang.Exception

deleteAdditionalQualifierFromExperiment

public void deleteAdditionalQualifierFromExperiment(long expId,
                                                    long qualifierId)
                                             throws java.lang.Exception
Throws:
java.lang.Exception

deleteExperiment

public void deleteExperiment(long expId)
                      throws java.lang.Exception
Throws:
java.lang.Exception

deleteExperimentalFactorFromExperiment

public void deleteExperimentalFactorFromExperiment(long expId,
                                                   long factorId)
                                            throws java.lang.Exception
Throws:
java.lang.Exception

deletePublicationFromExperiment

public void deletePublicationFromExperiment(long experimentId,
                                            long publicationId)
                                     throws java.lang.Exception
Throws:
java.lang.Exception

deleteQualityControlFromExperiment

public void deleteQualityControlFromExperiment(long expId,
                                               long qualityId)
                                        throws java.lang.Exception
Throws:
java.lang.Exception

searchExperiments

public ExperimentDesc[] searchExperiments(ExperimentSearchCriteria criteria,
                                          int pageSize,
                                          int pageNum)
                                   throws java.lang.Exception
Throws:
java.lang.Exception

searchExperiments

public ExperimentDesc[] searchExperiments(ExperimentSearchCriteria criteria)
                                   throws GeneralException
Throws:
GeneralException

updateAdditionalQualifier

public void updateAdditionalQualifier(long expId,
                                      AdditionalQualifierData qualifierData)
                               throws java.lang.Exception
Throws:
java.lang.Exception

updateExperiment

public void updateExperiment(ExperimentData expData)
                      throws java.lang.Exception
Throws:
java.lang.Exception

updateExperimentalFactors

public void updateExperimentalFactors(long expId,
                                      ExperimentalFactorData[] factorData)
                               throws java.lang.Exception
Throws:
java.lang.Exception

updatePublication

public void updatePublication(long expId,
                              PublicationData pubData)
                       throws java.lang.Exception
Throws:
java.lang.Exception

updateQualityControl

public void updateQualityControl(long expId,
                                 QualityControlData qualityControl)
                          throws java.lang.Exception
Throws:
java.lang.Exception

getExperimentView

public ExperimentView getExperimentView(long expId)
                                 throws java.lang.Exception
Throws:
java.lang.Exception

getExperiment

public ExperimentData getExperiment(long expId)
                             throws java.lang.Exception
Throws:
java.lang.Exception

addAdditionalDataProcessing

public void addAdditionalDataProcessing(long expId,
                                        AdditionalDataProcessingData data)
                                 throws java.lang.Exception
Throws:
java.lang.Exception

addAdditionalUploadedFile

public void addAdditionalUploadedFile(long expId,
                                      AdditionalUploadedFileData data)
                               throws java.lang.Exception
Throws:
java.lang.Exception

getAdditionalUploadedFile

public AdditionalUploadedFileData getAdditionalUploadedFile(long id)
                                                     throws java.lang.Exception
Throws:
java.lang.Exception

deleteAdditionalUploadedFileFromExperiment

public void deleteAdditionalUploadedFileFromExperiment(long expId,
                                                       long fileId)
                                                throws java.lang.Exception
Throws:
java.lang.Exception

getAdditionalDataProcessing

public AdditionalDataProcessingData getAdditionalDataProcessing(long id)
                                                         throws java.lang.Exception
Throws:
java.lang.Exception

deleteAdditionalDataProcessingFromExperiment

public void deleteAdditionalDataProcessingFromExperiment(long expId,
                                                         long dataId)
                                                  throws java.lang.Exception
Throws:
java.lang.Exception

lockExperiment

public void lockExperiment(long expId)
                    throws java.lang.Exception
Throws:
java.lang.Exception

addFactorValue

public long addFactorValue(long experimentalFactorId,
                           FactorValueData valueData)
                    throws java.lang.Exception
Throws:
java.lang.Exception

deleteFactorValueFromExperimentalFactor

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

deleteHybridizationFileUploadFromExperiment

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

getFactorValues

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

submitMAGEMLFile

public void submitMAGEMLFile(java.lang.String magemlFilePathName)
                      throws java.lang.Exception
Throws:
java.lang.Exception

submitHybridizationFileUploadsForParsing

public void submitHybridizationFileUploadsForParsing(long experimentId,
                                                     long[] hybUploadIds)
                                              throws java.lang.Exception
Throws:
java.lang.Exception

updateExperimentalFactor

public void updateExperimentalFactor(long experimentId,
                                     ExperimentalFactorData factor)
                              throws java.lang.Exception
Throws:
java.lang.Exception

getInputFilesDirectory

public java.lang.String getInputFilesDirectory()
                                        throws java.lang.Exception
Throws:
java.lang.Exception

getDataFilesDirectory

public java.lang.String getDataFilesDirectory(long experimentId)
                                       throws java.lang.Exception
Throws:
java.lang.Exception

getInputFilesDirectory

public java.lang.String getInputFilesDirectory(long experimentId)
                                        throws java.lang.Exception
Use to get directory for download files. Same as public ftp upload for now.

Throws:
java.lang.Exception

getLatestMAGEML

public FileData getLatestMAGEML(long experimentId)
                         throws java.lang.Exception
Throws:
java.lang.Exception

submitMAGEMLGeneration

public void submitMAGEMLGeneration(long experimentId)
                            throws java.lang.Exception
Throws:
java.lang.Exception

checkBatchDownloadFile

public boolean checkBatchDownloadFile(long experimentId,
                                      java.lang.String fileType)
                               throws java.lang.Exception
Throws:
java.lang.Exception

updateProtocolApplication

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

loadInformation

public ExperimentCleaningConfiguration loadInformation(ExperimentCleaningConfiguration configuration)
                                                throws java.lang.Exception
Throws:
java.lang.Exception

deleteExperiment

public ExperimentDeletionResult deleteExperiment(ExperimentData experimentData)
                                          throws java.lang.Exception
Throws:
java.lang.Exception

deleteHybridizations

public HybridizationDeletionResult deleteHybridizations(HybridizationDeletionConfiguration configuration)
                                                 throws java.lang.Exception
Throws:
java.lang.Exception