|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectgov.nih.nci.caarray.services.util.AbstractSessionBean
gov.nih.nci.caarray.services.biomaterial.ejb.BioMaterialManagerEJB
public class BioMaterialManagerEJB
BioMaterialManagerEJB
Field Summary |
---|
Fields inherited from class gov.nih.nci.caarray.services.util.AbstractSessionBean |
---|
logger_, sessionCtx_ |
Constructor Summary | |
---|---|
BioMaterialManagerEJB()
|
Method Summary | |
---|---|
long |
addBioSample(BioSampleData bioSampleData)
Adds the specified Biosample to the persistence store |
long |
addBioSource(BioSourceData bioSourceData,
VocabData[] characteristics)
Adds the specified BioSource to the persistence store |
long |
addTreatmentToBioSample(long bioSampleId,
TreatmentData treatmentData)
|
long |
addTreatmentToLabeledExtract(long labeledExtractId,
TreatmentData treatmentData)
|
long |
copyLabeledExtract(long labeledExtractId,
java.lang.String newLabeledExtractName)
Makes a copy of the given biomaterial including all the associated parent objects and treatments recursively. |
void |
deleteBioSample(long id)
Deletes a BioSample |
void |
deleteBioSource(long id)
Deletes a BioSource |
void |
deleteLabeledExtract(long id)
Deletes a LabeledExtract |
void |
deleteTreatmentFromBioMaterial(long bioMaterialId,
long treatmentId)
Deletes a treatment from a biomaterial |
long |
duplicateBioSample(long sourceBioSampleId,
java.lang.String newBioSampleName)
Makes a copy of the given biomaterial. |
long |
duplicateBioSource(long sourceBioSourceId,
java.lang.String newBioSourceName)
Applies the specified treatment to produce the specified output Makes a copy of the given biomaterial. |
long |
duplicateLabeledExtract(long labeledExtractId,
java.lang.String newLabeledExtractName)
Makes a copy of the given biomaterial. |
void |
ejbCreate()
|
void |
ejbRemove()
called when remove method is called. |
BioMaterialData |
getBioMaterial(long id)
Retrieve BioMaterial |
BioSampleData |
getBioSample(long id)
Retrieves the BioSampleData object from the persistence store. |
BioSampleView |
getBioSampleView(long id)
Retrieves the BioSampleData object from the persistence store. |
BioSourceData |
getBioSource(long id)
Retrieves the BioSourceData object from the persistence store. |
BioSourceView |
getBioSourceView(long id)
Retrieves the BioSourceView object from the persistence store. |
LabeledExtractData |
getLabeledExtract(long id)
|
LabeledExtractView |
getLabeledExtractView(long id)
Retrieves the LabeledExtractView object from the persistence store. |
TreatmentData |
getTreatment(long id)
Retrieves the TreatmentData object from the persistence store. |
TreatmentData[] |
getTreatments(long bioMaterialId)
|
long |
labelBioSample(TreatmentData labelingTreatment,
LabeledExtractData extractData)
Labels a BioMaterial to create a LabeledExtract. |
long |
poolBioSamples(TreatmentData poolingTreatment,
BioSampleData outputBioSample)
Pools bioMaterials into a single biomaterial |
BioMaterialDesc[] |
searchBioMaterials(BioMaterialSearchCriteria criteria)
Searches BioMaterials |
BioSampleDesc[] |
searchBioSamples(BioMaterialSearchCriteria criteria)
Searches BioSamples |
BioSampleDesc[] |
searchBioSamples(BioMaterialSearchCriteria criteria,
boolean ownerOnly)
Searches BioSamples |
BioSampleDesc[] |
searchBioSamples(BioMaterialSearchCriteria criteria,
int pageSize,
int pageNum)
Searches BioSamples |
BioSampleDesc[] |
searchBioSamples(BioMaterialSearchCriteria criteria,
int pageSize,
int pageNum,
boolean ownerOnly)
Searches BioSamples |
BioSampleDesc[] |
searchBioSamplesShallow(BioMaterialSearchCriteria criteria)
Shallow search for BioSamples |
BioSampleDesc[] |
searchBioSamplesShallow(BioMaterialSearchCriteria criteria,
boolean ownerOnly)
Shallow search for BioSamples |
BioSourceDesc[] |
searchBioSources(BioMaterialSearchCriteria criteria)
Searches BioSources |
BioSourceDesc[] |
searchBioSources(BioMaterialSearchCriteria criteria,
boolean ownerOnly)
Searches BioSources |
BioSourceDesc[] |
searchBioSources(BioMaterialSearchCriteria criteria,
int pageSize,
int pageNum)
Searches BioSources |
BioSourceDesc[] |
searchBioSources(BioMaterialSearchCriteria criteria,
int pageSize,
int pageNum,
boolean ownerOnly)
Searches BioSources |
BioSourceDesc[] |
searchBioSourcesShallow(BioMaterialSearchCriteria criteria)
Shallow search for BioSources |
BioSourceDesc[] |
searchBioSourcesShallow(BioMaterialSearchCriteria criteria,
boolean ownerOnly)
Shallow search for BioSources |
LabeledExtractDesc[] |
searchLabeledExtracts(BioMaterialSearchCriteria criteria)
Search Label Extract |
LabeledExtractDesc[] |
searchLabeledExtracts(BioMaterialSearchCriteria criteria,
int pageSize,
int pageNum)
Search Label Extract |
LabeledExtractDesc[] |
searchLabeledExtractsShallow(BioMaterialSearchCriteria criteria)
Shallow search for Label Extract |
long[] |
splitBioSample(TreatmentData splittingTreatment,
SplitBioSampleData[] splitBioSamples)
Splits a given bio sample to produce new bio samples represented by the specified output bio samples. |
long |
treatBioMaterial(TreatmentData[] treatmentData,
BioMaterialData outputBioMaterialData)
Applies the specified series of treatments to produce the specified output biomaterial. |
long |
treatBioMaterial(TreatmentData treatmentData,
BioMaterialData outputBioMaterialData)
Applies the specified treatment to produce the specified output biomaterial. |
void |
updateBioMaterialCharacteristics(long bioSourceId,
VocabData[] characteristics)
Performs the following: Update the characteristics with the new data if they exist (ID > 0) and are currently associated with the specified BioMaterial . |
void |
updateBioSample(BioSampleData bioSampleData)
Updates BioSample |
void |
updateBioSource(BioSourceData bioSourceData)
Updates BioSource |
void |
updateLabeledExtract(TreatmentData labelingTreatment,
LabeledExtractData extractData)
Updates LabeledExtract |
void |
updateTreatment(TreatmentData treatmentData)
Updates Treatment |
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 |
---|
public BioMaterialManagerEJB()
Method Detail |
---|
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 BioSourceView getBioSourceView(long id) throws java.lang.Exception
BioSourceView
object from the persistence store.
BioSourceView
object which ID matches the
specified ID or null otherwise.
java.lang.Exception
public BioMaterialData getBioMaterial(long id) throws java.lang.Exception
java.lang.Exception
public BioSourceData getBioSource(long id) throws java.lang.Exception
BioSourceData
object from the persistence store.
BioSourceData
object which ID matches the
specified ID or null otherwise.
java.lang.Exception
public BioSampleView getBioSampleView(long id) throws java.lang.Exception
BioSampleData
object from the persistence store.
BioSampleData
object which ID matches the
specified ID or null otherwise.
java.lang.Exception
public BioSampleData getBioSample(long id) throws java.lang.Exception
BioSampleData
object from the persistence store.
BioSampleData
object which ID matches the
specified ID or null otherwise.
java.lang.Exception
public TreatmentData getTreatment(long id) throws java.lang.Exception
TreatmentData
object from the persistence store.
TreatmentData
object which ID matches the
specified ID or null otherwise.
java.lang.Exception
public LabeledExtractView getLabeledExtractView(long id) throws java.lang.Exception
LabeledExtractView
object from the persistence store.
LabeledExtractView
object which ID matches the
specified ID or null otherwise.
java.lang.Exception
public LabeledExtractData getLabeledExtract(long id) throws java.lang.Exception
java.lang.Exception
public void updateBioSource(BioSourceData bioSourceData) throws java.lang.Exception
java.lang.Exception
public void updateBioSample(BioSampleData bioSampleData) throws java.lang.Exception
java.lang.Exception
public void updateTreatment(TreatmentData treatmentData) throws java.lang.Exception
java.lang.Exception
public void updateLabeledExtract(TreatmentData labelingTreatment, LabeledExtractData extractData) throws java.lang.Exception
extractData
- - The labeled extract to be updatedlabelingData
- - The labeling treatment that is associated with
the specified labeled extract to be updated as well
AccessDeniedException
- - If the current user is not authorized
to access the specified objects
ObjectNotExistException
- - If either the extract or treatment
is null or its ID is invalid.
GeneralException
- - When network communication or database error
occurs.
java.lang.Exception
public long addBioSource(BioSourceData bioSourceData, VocabData[] characteristics) throws java.lang.Exception
BioSource
to the persistence store
java.lang.Exception
public long addBioSample(BioSampleData bioSampleData) throws java.lang.Exception
Biosample
to the persistence store
java.lang.Exception
public long duplicateBioSource(long sourceBioSourceId, java.lang.String newBioSourceName) throws java.lang.Exception
java.lang.Exception
public long duplicateBioSample(long sourceBioSampleId, java.lang.String newBioSampleName) throws java.lang.Exception
java.lang.Exception
public long duplicateLabeledExtract(long labeledExtractId, java.lang.String newLabeledExtractName) throws java.lang.Exception
java.lang.Exception
public long copyLabeledExtract(long labeledExtractId, java.lang.String newLabeledExtractName) throws java.lang.Exception
java.lang.Exception
public TreatmentData[] getTreatments(long bioMaterialId) throws java.lang.Exception
java.lang.Exception
public long treatBioMaterial(TreatmentData treatmentData, BioMaterialData outputBioMaterialData) throws java.lang.Exception
java.lang.Exception
public long treatBioMaterial(TreatmentData[] treatmentData, BioMaterialData outputBioMaterialData) throws java.lang.Exception
java.lang.Exception
public long addTreatmentToBioSample(long bioSampleId, TreatmentData treatmentData) throws java.lang.Exception
java.lang.Exception
public long addTreatmentToLabeledExtract(long labeledExtractId, TreatmentData treatmentData) throws java.lang.Exception
java.lang.Exception
public long[] splitBioSample(TreatmentData splittingTreatment, SplitBioSampleData[] splitBioSamples) throws java.lang.Exception
BioSampleData
's
may contain name, description and measurement.
splittingTreatment
- - The treatment representing the splitting action.splitBioSamples
- - An array of new SplitBioSampleData
's
produced by the splitting treatment. The individual SplitBioSampleData
must contain at least name, description, measurement, and the parent
BioMaterial's ID.
java.lang.Exception
public long poolBioSamples(TreatmentData poolingTreatment, BioSampleData outputBioSample) throws java.lang.Exception
java.lang.Exception
public long labelBioSample(TreatmentData labelingTreatment, LabeledExtractData extractData) throws java.lang.Exception
extractData
- - The labeled extract to be addedlabelingData
- - The labeling treatment associated with the labeled
java.lang.Exception
public BioMaterialDesc[] searchBioMaterials(BioMaterialSearchCriteria criteria) throws java.lang.Exception
java.lang.Exception
public BioSourceDesc[] searchBioSources(BioMaterialSearchCriteria criteria, boolean ownerOnly) throws java.lang.Exception
java.lang.Exception
public BioSourceDesc[] searchBioSourcesShallow(BioMaterialSearchCriteria criteria) throws java.lang.Exception
java.lang.Exception
public BioSourceDesc[] searchBioSourcesShallow(BioMaterialSearchCriteria criteria, boolean ownerOnly) throws java.lang.Exception
java.lang.Exception
public BioSourceDesc[] searchBioSources(BioMaterialSearchCriteria criteria) throws java.lang.Exception
java.lang.Exception
public BioSourceDesc[] searchBioSources(BioMaterialSearchCriteria criteria, int pageSize, int pageNum) throws java.lang.Exception
java.lang.Exception
public BioSourceDesc[] searchBioSources(BioMaterialSearchCriteria criteria, int pageSize, int pageNum, boolean ownerOnly) throws java.lang.Exception
java.lang.Exception
public BioSampleDesc[] searchBioSamplesShallow(BioMaterialSearchCriteria criteria) throws java.lang.Exception
java.lang.Exception
public BioSampleDesc[] searchBioSamplesShallow(BioMaterialSearchCriteria criteria, boolean ownerOnly) throws java.lang.Exception
java.lang.Exception
public BioSampleDesc[] searchBioSamples(BioMaterialSearchCriteria criteria) throws java.lang.Exception
java.lang.Exception
public BioSampleDesc[] searchBioSamples(BioMaterialSearchCriteria criteria, boolean ownerOnly) throws java.lang.Exception
java.lang.Exception
public BioSampleDesc[] searchBioSamples(BioMaterialSearchCriteria criteria, int pageSize, int pageNum) throws java.lang.Exception
java.lang.Exception
public BioSampleDesc[] searchBioSamples(BioMaterialSearchCriteria criteria, int pageSize, int pageNum, boolean ownerOnly) throws java.lang.Exception
java.lang.Exception
public LabeledExtractDesc[] searchLabeledExtracts(BioMaterialSearchCriteria criteria, int pageSize, int pageNum) throws java.lang.Exception
java.lang.Exception
public LabeledExtractDesc[] searchLabeledExtracts(BioMaterialSearchCriteria criteria) throws java.lang.Exception
java.lang.Exception
public LabeledExtractDesc[] searchLabeledExtractsShallow(BioMaterialSearchCriteria criteria) throws java.lang.Exception
java.lang.Exception
public void updateBioMaterialCharacteristics(long bioSourceId, VocabData[] characteristics) throws java.lang.Exception
BioMaterial
.
bioSourceId
- - The BioSource
whose characteristics
are to be updatedcharacteristics
- - The characteristics to be updated.
java.lang.Exception
public void deleteTreatmentFromBioMaterial(long bioMaterialId, long treatmentId) throws java.lang.Exception
java.lang.Exception
public void deleteBioSource(long id) throws java.lang.Exception
java.lang.Exception
public void deleteBioSample(long id) throws java.lang.Exception
java.lang.Exception
public void deleteLabeledExtract(long id) throws java.lang.Exception
java.lang.Exception
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |