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java.lang.Objectgov.nih.nci.caarray.services.util.AbstractSessionBean
gov.nih.nci.caarray.services.arraydesign.ejb.ArrayDesignManagerEJB
public class ArrayDesignManagerEJB
ArrayDesignManagerEJB
Field Summary |
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Fields inherited from class gov.nih.nci.caarray.services.util.AbstractSessionBean |
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logger_, sessionCtx_ |
Constructor Summary | |
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ArrayDesignManagerEJB()
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Method Summary | |
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long |
addArrayDesign(ArrayDesignData arrayDesignData)
Add the specified ArrayDesign to the persistence store |
void |
addCompositeGroup(long arraydesignId,
long compositegroupId)
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void |
addDesignProviderRole(long arrayDesignId,
DesignProviderRoleData providerRoleData)
Associates a provider with an ArrayDesign |
void |
addFeatureGroup(long arraydesignId,
long featuregroupId)
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long |
addProtocolApplication(long arrayDesignId,
ProtocolApplicationData protAppData)
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void |
addReporterGroup(long arraydesignId,
long reportergroupId)
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void |
deleteArrayDesign(long arrayDesignId)
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void |
deleteProtocolApplicationFromArrayDesign(long arrayDesignId,
long protAppId)
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void |
disableConstraintsAndIndexes()
Disables array design indexes and constraints to enable fast loading of array designs. |
void |
ejbCreate()
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void |
ejbRemove()
called when remove method is called. |
void |
enableConstraintsAndIndexes()
Re-enables array design indexes and constraints disabled in disableConstraintsAndIndexes . |
java.lang.String |
generateMage(ArrayDesignDesc designDesc)
Generates a MAGE-ML file for the array design given. |
ArrayDesignData |
getArrayDesign(long arrayDesignId)
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java.util.List |
getArrayDesignsToReload()
Returns array designs that should be reloaded. |
ArrayDesignUploadedFileData |
getArrayDesignUploadedFileData(long arrayDesignId)
Gets the information about the uploaded arraydesign files for the specified ArrayDesign. |
ArrayDesignView |
getArrayDesignView(long arrayDesignId)
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FileData |
getGALFile(long arrayDesignId)
Gets the information about the gal files for the specified ArrayDesign. |
FileData |
getMAGEML(long arrayDesignId)
Gets the information about the MAGEML for the specified ArrayDesign. |
boolean |
isArrayDesignProvidedByAffymetrix(long arrayDesignId)
Checks if the specified ArrayDesign was made/provided by Affymetrix. |
void |
reloadArrayDesign(ArrayDesignDesc arrayDesign,
int timeoutMinutes)
Reloads design information for existing array designs. |
void |
removeCompositeGroupFromArrayDesign(long arrayDesignId,
long compositeGroupId)
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void |
removeDesignElements(ArrayDesignDesc design,
int timeoutMinutes)
Removes the design elements associated with an array design in preparation for reloading. |
void |
removeDesignProviderFromArrayDesign(long arrayDesignId,
long providerId)
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void |
removeFeatureGroupFromArrayDesign(long arrayDesignId,
long featureGroupId)
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void |
removeReporterGroupFromArrayDesign(long arrayDesignId,
long reporterGroupId)
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ArrayDesignDesc[] |
search(ArrayDesignSearchCriteria searchCriteria)
Searches ArrayDesign 's that match the specifed
ArrayDesignSearchCriteria . |
void |
submitMAGEMLGeneration(long arrayDesignId)
Submits a MAGEML generation message to the responsible Message Driven Bean to generate MAGEML for the specified ArrayDesign. |
void |
updateArrayDesign(ArrayDesignData arrayDesignData)
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void |
updateArrayDesignVisibility(ArrayDesignData arrayDesignData)
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Methods inherited from class gov.nih.nci.caarray.services.util.AbstractSessionBean |
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disableAndRememberPreviousValueForCollectionDescriptorCascadeRetrieve, disableAndRememberPreviousValueForObjectDescriptorCascadeRetrieve, ejbActivate, ejbPassivate, getUserTransaction, resetCollectionDescriptorCascadeToPreviousValue, resetObjectDescriptorCascadeToPreviousValue, setSessionContext |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface javax.ejb.SessionBean |
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ejbActivate, ejbPassivate, setSessionContext |
Constructor Detail |
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public ArrayDesignManagerEJB()
Method Detail |
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public void ejbCreate() throws java.rmi.RemoteException, javax.ejb.CreateException
ejbCreate
in class AbstractSessionBean
javax.ejb.CreateException
java.rmi.RemoteException
public void ejbRemove() throws javax.ejb.EJBException, java.rmi.RemoteException
ejbRemove
in interface javax.ejb.SessionBean
ejbRemove
in class AbstractSessionBean
javax.ejb.EJBException
java.rmi.RemoteException
public ArrayDesignData getArrayDesign(long arrayDesignId) throws java.lang.Exception
java.lang.Exception
public ArrayDesignUploadedFileData getArrayDesignUploadedFileData(long arrayDesignId) throws java.lang.Exception
java.lang.Exception
public ArrayDesignView getArrayDesignView(long arrayDesignId) throws java.lang.Exception
java.lang.Exception
public long addArrayDesign(ArrayDesignData arrayDesignData) throws InsertObjectException, GeneralException
ArrayDesign
to the persistence store
InsertObjectException
GeneralException
public void updateArrayDesign(ArrayDesignData arrayDesignData) throws java.lang.Exception
java.lang.Exception
public void deleteArrayDesign(long arrayDesignId) throws java.lang.Exception
java.lang.Exception
public void updateArrayDesignVisibility(ArrayDesignData arrayDesignData) throws java.lang.Exception
java.lang.Exception
public ArrayDesignDesc[] search(ArrayDesignSearchCriteria searchCriteria) throws java.lang.Exception
ArrayDesign
's that match the specifed
ArrayDesignSearchCriteria
.
ArrayDesign
objects or null
otherwise.
java.lang.Exception
public void addCompositeGroup(long arraydesignId, long compositegroupId) throws java.lang.Exception
java.lang.Exception
public void removeCompositeGroupFromArrayDesign(long arrayDesignId, long compositeGroupId) throws java.lang.Exception
java.lang.Exception
public void addFeatureGroup(long arraydesignId, long featuregroupId) throws java.lang.Exception
java.lang.Exception
public void removeFeatureGroupFromArrayDesign(long arrayDesignId, long featureGroupId) throws java.lang.Exception
java.lang.Exception
public void addReporterGroup(long arraydesignId, long reportergroupId) throws java.lang.Exception
java.lang.Exception
public void removeReporterGroupFromArrayDesign(long arrayDesignId, long reporterGroupId) throws java.lang.Exception
java.lang.Exception
public void addDesignProviderRole(long arrayDesignId, DesignProviderRoleData providerRoleData) throws java.lang.Exception
java.lang.Exception
public void removeDesignProviderFromArrayDesign(long arrayDesignId, long providerId) throws java.lang.Exception
java.lang.Exception
public long addProtocolApplication(long arrayDesignId, ProtocolApplicationData protAppData) throws java.lang.Exception
java.lang.Exception
public void deleteProtocolApplicationFromArrayDesign(long arrayDesignId, long protAppId) throws java.lang.Exception
java.lang.Exception
public void submitMAGEMLGeneration(long arrayDesignId) throws java.lang.Exception
java.lang.Exception
public boolean isArrayDesignProvidedByAffymetrix(long arrayDesignId) throws java.lang.Exception
arrayDesignId
- - The ID of the ArrayDesign being checked
AccessDeniedException
ObjectNotExistException
GeneralException
java.lang.Exception
public FileData getMAGEML(long arrayDesignId) throws java.lang.Exception
arrayDesignId
- - The ArrayDesign for which the MAGEML is available.
FileData
object containing information
about the MAGEML for this ArrayDesign.
java.lang.Exception
public FileData getGALFile(long arrayDesignId) throws java.lang.Exception
java.lang.Exception
public java.util.List getArrayDesignsToReload() throws ArrayDesignDataSourceException
ArrayDesignDataSourceException
public void reloadArrayDesign(ArrayDesignDesc arrayDesign, int timeoutMinutes) throws java.lang.Exception
TransactionException
ArrayDesignDataSourceException
java.lang.Exception
public java.lang.String generateMage(ArrayDesignDesc designDesc) throws java.lang.Exception
java.lang.Exception
public void disableConstraintsAndIndexes() throws java.lang.Exception
ArrayDesignDataSourceException
java.lang.Exception
public void enableConstraintsAndIndexes() throws java.lang.Exception
disableConstraintsAndIndexes
.
ArrayDesignDataSourceException
java.lang.Exception
public void removeDesignElements(ArrayDesignDesc design, int timeoutMinutes) throws java.lang.Exception
ArrayDesignDataSourceException
java.lang.Exception
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