gov.nih.nci.caarray.services.mageml.ejb
Class MAGEMLManagerEJB

java.lang.Object
  extended by gov.nih.nci.caarray.services.util.AbstractSessionBean
      extended by gov.nih.nci.caarray.services.mageml.ejb.MAGEMLManagerEJB
All Implemented Interfaces:
java.io.Serializable, javax.ejb.EnterpriseBean, javax.ejb.SessionBean

public class MAGEMLManagerEJB
extends AbstractSessionBean
implements javax.ejb.SessionBean

MAGEMLManagerEJB

Author:
TranP
See Also:
Serialized Form

Field Summary
 
Fields inherited from class gov.nih.nci.caarray.services.util.AbstractSessionBean
logger_, sessionCtx_
 
Constructor Summary
MAGEMLManagerEJB()
           
 
Method Summary
 void clearCache()
          Flushes the OJB cache so that any updated data may be found after a caAMEL MAGE-ML import is performed.
 void ejbCreate()
           
 void ejbRemove()
          called when remove method is called.
 void exportArrayDesign(long arrayDesignId, java.lang.String outputPathName, boolean zip)
          Generates MAGEML for the specified ArrayDesign and zips it up in a file having the specified path.
 void exportExperiment(long experimentId, java.lang.String outputPathName, boolean zip)
          Generates MAGEML for the specified experiment and zips it up in a file having the specified path.
 void importArrayDesign(java.lang.String pathName, java.lang.String owner, ProtectionGroupData[] protectionGroups)
           
 void importExperiment(java.lang.String directory, java.lang.String[] fileNames, java.lang.String owner, ProtectionGroupData[] protectionGroups)
           
 void importExperiment(java.lang.String pathName, java.lang.String owner, ProtectionGroupData[] protectionGroups)
           
 void importFileData(java.util.Set fileUploadEntryIds, java.lang.String username)
          Queues the file uploads corresponding to the ids given for data parsing and storage.
 void importProtocols(java.lang.String pathName, java.lang.String owner, ProtectionGroupData[] protectionGroups)
          For testing only
 
Methods inherited from class gov.nih.nci.caarray.services.util.AbstractSessionBean
disableAndRememberPreviousValueForCollectionDescriptorCascadeRetrieve, disableAndRememberPreviousValueForObjectDescriptorCascadeRetrieve, ejbActivate, ejbPassivate, getUserTransaction, resetCollectionDescriptorCascadeToPreviousValue, resetObjectDescriptorCascadeToPreviousValue, setSessionContext
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface javax.ejb.SessionBean
ejbActivate, ejbPassivate, setSessionContext
 

Constructor Detail

MAGEMLManagerEJB

public MAGEMLManagerEJB()
Method Detail

ejbCreate

public void ejbCreate()
               throws java.rmi.RemoteException,
                      javax.ejb.CreateException
Overrides:
ejbCreate in class AbstractSessionBean
Throws:
javax.ejb.CreateException
java.rmi.RemoteException

ejbRemove

public void ejbRemove()
               throws javax.ejb.EJBException,
                      java.rmi.RemoteException
called when remove method is called.

Specified by:
ejbRemove in interface javax.ejb.SessionBean
Overrides:
ejbRemove in class AbstractSessionBean
Throws:
javax.ejb.EJBException
java.rmi.RemoteException

exportExperiment

public void exportExperiment(long experimentId,
                             java.lang.String outputPathName,
                             boolean zip)
                      throws java.lang.Exception
Generates MAGEML for the specified experiment and zips it up in a file having the specified path.

Parameters:
experimentId -
outputPathName - - The output MAGEML file which has the .xml extension. If not, the .xml extension is automatically added.
zip - - True to compress the output file in a zip file with the same file name having the .zip extension. False to ignore the compression.
Throws:
java.lang.Exception

importExperiment

public void importExperiment(java.lang.String pathName,
                             java.lang.String owner,
                             ProtectionGroupData[] protectionGroups)
                      throws java.lang.Exception
Parameters:
directory -
Throws:
AccessDeniedException
GeneralException
java.lang.Exception

importExperiment

public void importExperiment(java.lang.String directory,
                             java.lang.String[] fileNames,
                             java.lang.String owner,
                             ProtectionGroupData[] protectionGroups)
                      throws AccessDeniedException,
                             GeneralException
Parameters:
directory -
fileNames -
Throws:
AccessDeniedException
GeneralException

importArrayDesign

public void importArrayDesign(java.lang.String pathName,
                              java.lang.String owner,
                              ProtectionGroupData[] protectionGroups)

exportArrayDesign

public void exportArrayDesign(long arrayDesignId,
                              java.lang.String outputPathName,
                              boolean zip)
                       throws java.lang.Exception
Generates MAGEML for the specified ArrayDesign and zips it up in a file having the specified path.

Parameters:
arrayDesignId -
outputPathName - - The output MAGEML file which has the .xml extension. If not, the .xml extension is automatically added.
zip - - True to compress the output file in a zip file with the same file name having the .zip extension. False to ignore the compression.
Throws:
java.lang.Exception

clearCache

public void clearCache()
Flushes the OJB cache so that any updated data may be found after a caAMEL MAGE-ML import is performed.


importFileData

public void importFileData(java.util.Set fileUploadEntryIds,
                           java.lang.String username)
Queues the file uploads corresponding to the ids given for data parsing and storage.


importProtocols

public void importProtocols(java.lang.String pathName,
                            java.lang.String owner,
                            ProtectionGroupData[] protectionGroups)
For testing only