gov.nih.nci.caarray.services.fileupload2
Class FileUploadManagerDB

java.lang.Object
  extended by gov.nih.nci.caarray.services.util.db.ManagerDB
      extended by gov.nih.nci.caarray.services.fileupload2.FileUploadManagerDB

public class FileUploadManagerDB
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
FileUploadManagerDB()
          Default Constructor
 
Method Summary
 long addArrayDesignFileParsingEntry(ArrayDesignFileParsingEntry fileParsingEntry)
           
 long addArrayDesignFileUploadEntry(ArrayDesignFileUploadEntry fileUploadEntry, java.lang.String errorDescription)
           
 long addArrayDesignFileUploadGroup(ArrayDesignFileUploadGroup fileUploadGroup)
           
 long addCAFileUploadEntry(CAFileUploadEntry fileUploadEntry)
           
 long addHybridizationFileParsingEntry(HybridizationFileParsingEntry fileParsingEntry)
           
 boolean addHybridizationFileParsingEntryToFileUploadEntry(HybridizationFileUploadEntry fileUploadEntry)
           
 long addHybridizationFileUploadEntry(HybridizationFileUploadEntry fileUploadEntry, java.lang.String errorDescription)
           
 long addHybridizationFileUploadGroup(HybridizationFileUploadGroup fileUploadGroup)
           
 long addMAGEMLFileUploadEntry(MAGEMLFileUploadEntry fileUploadEntry, java.lang.String errorDescription)
           
 void close()
          Close database connection.
 int countHybridizationFileUploadEntries(long experimentId)
           
 boolean deleteAnnotationFromHybridizationFileUploadEntry(long fileUploadEntryId)
           
 void deleteArrayDesignFileUploadGroup(long fileUploadGroupId)
           
 void deleteArrayDesignFileUploadGroupByArrayDesign(long arrayDesignId)
          Delete the fileUploadGroup that maintains the uploaded files for the specified ArrayDesign.
 boolean deleteHybridizationFileUploadEntry(long fileUploadEntryId)
           
 void deleteHybridizationFileUploadGroup(long fileUploadGroupId)
           
 void formatForView(HybridizationFileUploadEntry entry)
          Sets root physical bio assay and expected protocols prior to handing this object off for copying into a data or view object for display.
 HybridizationFileUploadEntry[] getAllHybridizationFileUploadEntries()
           
 ArrayDesignFileUploadEntry getArrayDesignFileUploadEntry(long fileUploadEntryId)
           
 ArrayDesignFileUploadEntry getArrayDesignFileUploadEntryByArrayDesignId(long arrayDesignId)
           
 ArrayDesignFileUploadGroup getArrayDesignFileUploadGroup(long arrayDesignFileUploadGroupId)
           
 ArrayDesignFileUploadGroup getArrayDesignFileUploadGroupByArrayDesign(long arrayDesignId)
           
 FileUploadHistory[] getFileHistoryEntries(FileUploadHistorySearchCriteria criteria)
          Gets MAGEMLFileUploadEntries.
 FileType getFileTypeById(java.lang.String fileTypeId)
           
 FileUploadEntry getFileUploadEntry(long fileUploadEntryId)
           
 HybridizationFileParsingEntry getHybridizationFileParsingEntry(long hybridizationFileParsingEntryId)
           
 HybridizationFileUploadEntry[] getHybridizationFileUploadEntries(long experimentId)
           
 HybridizationFileUploadEntry getHybridizationFileUploadEntry(long hybridizationFileUploadEntryId)
           
 HybridizationFileUploadGroup getHybridizationFileUploadGroup(long hybridizationFileUploadGroupId)
           
 java.lang.String[] getHybridizationSoftwareNames()
          Retrieves the distinct list of creating software names from all FileTypes.
 MAGEMLFileUploadEntry[] getMAGEMLFileEntries(MAGEMLFileUploadSearchCriteria criteria)
          Gets MAGEMLFileUploadEntries.
 MAGEMLFileUploadEntry getMAGEMLFileUploadEntry(long fileUploadEntryId)
           
 void save(CAFileUploadEntry entry)
          Saves data for a CAFileUploadEntry without saving (linking only) any associated MAGE objects.
 void save(HybridizationFileUploadEntry fileUploadEntry)
          Saves data for a HybridizationFileUploadEntry without saving (linking only) any associated MAGE objects.
 void updateArrayDesignFileParsingEntry(ArrayDesignFileParsingEntry fileParsingEntry)
           
 void updateArrayDesignFileUploadEntry(ArrayDesignFileUploadEntry fileUploadEntry, java.lang.String errorDescription)
           
 void updateArrayDesignFileUploadGroup(ArrayDesignFileUploadGroup fileUploadGroup)
           
 void updateHybridizationFileParsingEntry(HybridizationFileParsingEntry fileParsingEntry)
           
 void updateHybridizationFileUploadEntry(HybridizationFileUploadEntry fileUploadEntry, boolean updateAnnotations, java.lang.String errorDescription)
           
 boolean updateHybridizationFileUploadEntryFactorValues(long hybridizationUploadEntryId, long[] channelOneFactorValues, long[] channelTwoFactorValues)
           
 void updateHybridizationFileUploadGroup(HybridizationFileUploadGroup fileUploadGroup)
           
 void updateHybridizationFileUploadGroup(HybridizationFileUploadGroup fileUploadGroup, boolean updateFileUploadEntriesWithAnnotations)
           
 void updateMAGEMLFileUploadEntry(MAGEMLFileUploadEntry fileUploadEntry, java.lang.String errorDescription)
           
 
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

FileUploadManagerDB

public FileUploadManagerDB()
Default Constructor

Method Detail

getHybridizationFileUploadGroup

public HybridizationFileUploadGroup getHybridizationFileUploadGroup(long hybridizationFileUploadGroupId)
                                                             throws java.lang.Exception
Throws:
java.lang.Exception

addArrayDesignFileUploadEntry

public long addArrayDesignFileUploadEntry(ArrayDesignFileUploadEntry fileUploadEntry,
                                          java.lang.String errorDescription)
                                   throws java.lang.Exception
Throws:
java.lang.Exception

getFileTypeById

public FileType getFileTypeById(java.lang.String fileTypeId)
                         throws java.lang.Exception
Throws:
java.lang.Exception

addCAFileUploadEntry

public long addCAFileUploadEntry(CAFileUploadEntry fileUploadEntry)
                          throws java.lang.Exception
Throws:
java.lang.Exception

addHybridizationFileUploadEntry

public long addHybridizationFileUploadEntry(HybridizationFileUploadEntry fileUploadEntry,
                                            java.lang.String errorDescription)
                                     throws java.lang.Exception
Throws:
java.lang.Exception

addHybridizationFileUploadGroup

public long addHybridizationFileUploadGroup(HybridizationFileUploadGroup fileUploadGroup)
                                     throws java.lang.Exception
Throws:
java.lang.Exception

updateHybridizationFileUploadGroup

public void updateHybridizationFileUploadGroup(HybridizationFileUploadGroup fileUploadGroup)
                                        throws java.lang.Exception
Throws:
java.lang.Exception

updateHybridizationFileUploadGroup

public void updateHybridizationFileUploadGroup(HybridizationFileUploadGroup fileUploadGroup,
                                               boolean updateFileUploadEntriesWithAnnotations)
                                        throws java.lang.Exception
Parameters:
fileUploadGroup -
updateFileUploadEntriesWithAnnotations -
Throws:
ObjectNotExistException
DBException
java.lang.Exception

deleteHybridizationFileUploadGroup

public void deleteHybridizationFileUploadGroup(long fileUploadGroupId)
                                        throws java.lang.Exception
Throws:
java.lang.Exception

getHybridizationFileUploadEntry

public HybridizationFileUploadEntry getHybridizationFileUploadEntry(long hybridizationFileUploadEntryId)
                                                             throws java.lang.Exception
Throws:
java.lang.Exception

getAllHybridizationFileUploadEntries

public HybridizationFileUploadEntry[] getAllHybridizationFileUploadEntries()
                                                                    throws java.lang.Exception
Throws:
java.lang.Exception

getFileUploadEntry

public FileUploadEntry getFileUploadEntry(long fileUploadEntryId)
                                   throws java.lang.Exception
Throws:
java.lang.Exception

getHybridizationFileUploadEntries

public HybridizationFileUploadEntry[] getHybridizationFileUploadEntries(long experimentId)
                                                                 throws java.lang.Exception
Throws:
java.lang.Exception

updateHybridizationFileUploadEntry

public void updateHybridizationFileUploadEntry(HybridizationFileUploadEntry fileUploadEntry,
                                               boolean updateAnnotations,
                                               java.lang.String errorDescription)
                                        throws java.lang.Exception
Throws:
java.lang.Exception

addHybridizationFileParsingEntryToFileUploadEntry

public boolean addHybridizationFileParsingEntryToFileUploadEntry(HybridizationFileUploadEntry fileUploadEntry)

getHybridizationFileParsingEntry

public HybridizationFileParsingEntry getHybridizationFileParsingEntry(long hybridizationFileParsingEntryId)
                                                               throws java.lang.Exception
Throws:
java.lang.Exception

addHybridizationFileParsingEntry

public long addHybridizationFileParsingEntry(HybridizationFileParsingEntry fileParsingEntry)
                                      throws java.lang.Exception
Throws:
java.lang.Exception

updateHybridizationFileParsingEntry

public void updateHybridizationFileParsingEntry(HybridizationFileParsingEntry fileParsingEntry)
                                         throws java.lang.Exception
Throws:
java.lang.Exception

getArrayDesignFileUploadGroup

public ArrayDesignFileUploadGroup getArrayDesignFileUploadGroup(long arrayDesignFileUploadGroupId)
                                                         throws java.lang.Exception
Throws:
java.lang.Exception

getArrayDesignFileUploadGroupByArrayDesign

public ArrayDesignFileUploadGroup getArrayDesignFileUploadGroupByArrayDesign(long arrayDesignId)
                                                                      throws java.lang.Exception
Throws:
java.lang.Exception

addArrayDesignFileUploadGroup

public long addArrayDesignFileUploadGroup(ArrayDesignFileUploadGroup fileUploadGroup)
                                   throws java.lang.Exception
Throws:
java.lang.Exception

updateArrayDesignFileUploadGroup

public void updateArrayDesignFileUploadGroup(ArrayDesignFileUploadGroup fileUploadGroup)
                                      throws java.lang.Exception
Throws:
java.lang.Exception

deleteArrayDesignFileUploadGroup

public void deleteArrayDesignFileUploadGroup(long fileUploadGroupId)
                                      throws java.lang.Exception
Throws:
java.lang.Exception

deleteArrayDesignFileUploadGroupByArrayDesign

public void deleteArrayDesignFileUploadGroupByArrayDesign(long arrayDesignId)
                                                   throws java.lang.Exception
Delete the fileUploadGroup that maintains the uploaded files for the specified ArrayDesign.

Parameters:
arrayDesignId -
Throws:
ObjectNotExistException
ObjectInUseException
DBException
java.lang.Exception

getMAGEMLFileUploadEntry

public MAGEMLFileUploadEntry getMAGEMLFileUploadEntry(long fileUploadEntryId)
                                               throws java.lang.Exception
Throws:
java.lang.Exception

addMAGEMLFileUploadEntry

public long addMAGEMLFileUploadEntry(MAGEMLFileUploadEntry fileUploadEntry,
                                     java.lang.String errorDescription)
                              throws java.lang.Exception
Throws:
java.lang.Exception

updateMAGEMLFileUploadEntry

public void updateMAGEMLFileUploadEntry(MAGEMLFileUploadEntry fileUploadEntry,
                                        java.lang.String errorDescription)
                                 throws java.lang.Exception
Throws:
java.lang.Exception

getArrayDesignFileUploadEntry

public ArrayDesignFileUploadEntry getArrayDesignFileUploadEntry(long fileUploadEntryId)
                                                         throws java.lang.Exception
Throws:
java.lang.Exception

updateArrayDesignFileUploadEntry

public void updateArrayDesignFileUploadEntry(ArrayDesignFileUploadEntry fileUploadEntry,
                                             java.lang.String errorDescription)
                                      throws java.lang.Exception
Throws:
java.lang.Exception

addArrayDesignFileParsingEntry

public long addArrayDesignFileParsingEntry(ArrayDesignFileParsingEntry fileParsingEntry)
                                    throws java.lang.Exception
Throws:
java.lang.Exception

updateArrayDesignFileParsingEntry

public void updateArrayDesignFileParsingEntry(ArrayDesignFileParsingEntry fileParsingEntry)
                                       throws java.lang.Exception
Throws:
java.lang.Exception

getHybridizationSoftwareNames

public java.lang.String[] getHybridizationSoftwareNames()
Retrieves the distinct list of creating software names from all FileTypes.

Returns:
- A String[] of creating software names.

updateHybridizationFileUploadEntryFactorValues

public boolean updateHybridizationFileUploadEntryFactorValues(long hybridizationUploadEntryId,
                                                              long[] channelOneFactorValues,
                                                              long[] channelTwoFactorValues)
                                                       throws java.lang.Exception
Throws:
java.lang.Exception

deleteHybridizationFileUploadEntry

public boolean deleteHybridizationFileUploadEntry(long fileUploadEntryId)
                                           throws java.lang.Exception
Throws:
java.lang.Exception

deleteAnnotationFromHybridizationFileUploadEntry

public boolean deleteAnnotationFromHybridizationFileUploadEntry(long fileUploadEntryId)
                                                         throws java.lang.Exception
Throws:
java.lang.Exception

countHybridizationFileUploadEntries

public int countHybridizationFileUploadEntries(long experimentId)
                                        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

getFileHistoryEntries

public FileUploadHistory[] getFileHistoryEntries(FileUploadHistorySearchCriteria criteria)
                                          throws java.lang.Exception
Gets MAGEMLFileUploadEntries.

Returns:
Throws:
java.lang.Exception

getMAGEMLFileEntries

public MAGEMLFileUploadEntry[] getMAGEMLFileEntries(MAGEMLFileUploadSearchCriteria criteria)
                                             throws java.lang.Exception
Gets MAGEMLFileUploadEntries.

Returns:
Throws:
java.lang.Exception

formatForView

public void formatForView(HybridizationFileUploadEntry entry)
Sets root physical bio assay and expected protocols prior to handing this object off for copying into a data or view object for display. This is necessary to account for more complex MAGE object graphs received during MAGE-ML import.

Parameters:
entry - the upload entry requiring reformatting.

save

public void save(HybridizationFileUploadEntry fileUploadEntry)
          throws java.lang.Exception
Saves data for a HybridizationFileUploadEntry without saving (linking only) any associated MAGE objects.

Parameters:
fileUploadEntry -
Throws:
java.lang.Exception

save

public void save(CAFileUploadEntry entry)
          throws java.lang.Exception
Saves data for a CAFileUploadEntry without saving (linking only) any associated MAGE objects.

Parameters:
entry -
Throws:
java.lang.Exception

getArrayDesignFileUploadEntryByArrayDesignId

public ArrayDesignFileUploadEntry getArrayDesignFileUploadEntryByArrayDesignId(long arrayDesignId)
                                                                        throws ObjectNotExistException,
                                                                               java.lang.Exception
Throws:
ObjectNotExistException
java.lang.Exception