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java.lang.Objectgov.nih.nci.caarray.services.util.AbstractSessionBean
gov.nih.nci.caarray.services.experiment.ejb.ExperimentManagerEJB
public class ExperimentManagerEJB
ExperimentManagerEJB
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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ExperimentManagerEJB()
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Method Summary | |
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void |
addAdditionalDataProcessing(long experimentId,
AdditionalDataProcessingData addDataProcessing)
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void |
addAdditionalQualifier(long experimentId,
AdditionalQualifierData qualifier)
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void |
addAdditionalUploadedFile(long experimentId,
AdditionalUploadedFileData uploadData)
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long |
addExperiment(ExperimentData experimentData,
ExperimentalFactorData[] factors)
Adds a new experiment. |
void |
addExperimentalFactors(long experimentId,
ExperimentalFactorData[] factorData)
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long |
addFactorValue(long experimentalFactorId,
FactorValueData valueData)
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long |
addHybridizationFileUpload(long experimentId,
HybridizationFileUploadData uploadData)
Deprecated. This method is replaced by FileUploadManagerEJB.addHybridizationFileUploadGroup |
HybridizationFileUploadData[] |
addHybridizationFileUploads(long experimentId,
HybridizationFileUploadData[] uploadData)
Deprecated. This method is replaced by FileUploadManagerEJB.addHybridizationFileUploadGroup |
long |
addPublication(long experimentId,
PublicationData pubData)
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void |
addQualityControl(long experimentId,
QualityControlData qualityControlData)
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boolean |
checkBatchDownloadFile(long experimentId,
java.lang.String fileExtension)
Check Batch Download Files are existing or not. |
void |
deleteAdditionalDataProcessingFromExperiment(long experimentId,
long id)
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void |
deleteAdditionalQualifierFromExperiment(long experimentId,
long id)
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void |
deleteAdditionalUploadedFileFromExperiment(long experimentId,
long id)
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ExperimentDeletionResult |
deleteExperiment(ExperimentData experimentData)
Deletes an experiment and associated files from the system. |
void |
deleteExperiment(long experimentId)
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void |
deleteExperimentalFactorFromExperiment(long experimentId,
long id)
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void |
deleteFactorValueFromExperimentalFactor(long experimentalFactorId,
long factorValueId)
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void |
deleteHybridizationFileUploadFromExperiment(long experimentId,
long id)
Deprecated. - No longer applicable |
HybridizationDeletionResult |
deleteHybridizations(HybridizationDeletionConfiguration configuration)
Deletes an experiment and associated files from the system. |
void |
deletePublicationFromExperiment(long experimentId,
long pubId)
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void |
deleteQualityControlFromExperiment(long experimentId,
long id)
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void |
ejbCreate()
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void |
ejbRemove()
called when remove method is called. |
AdditionalDataProcessingData |
getAdditionalDataProcessing(long id)
Retrieves the AdditionalDataProcessingData object from the persistence store. |
AdditionalDataProcessingData[] |
getAdditionalDataProcessings(long experimentId)
Retrieves the AdditionalDataProcessingData object from the persistence store. |
AdditionalUploadedFileData |
getAdditionalUploadedFile(long id)
Retrieves a AdditionalDataProcessingData object from the persistence store. |
AdditionalUploadedFileData[] |
getAdditionalUploadedFiles(long experimentId)
Retrieves the AdditionalDataProcessingData object from the persistence store. |
java.lang.String |
getDataFilesDirectory(long experimentId)
Gets the directory for storing additional uploaded files and and additional data processing files that are associated with an experiment. |
ExperimentData |
getExperiment(long id)
Retrieves the Experiment object from the persistence store. |
ExperimentalFactorData[] |
getExperimentalFactors(long experimentId)
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ExperimentView |
getExperimentView(long id)
Retrieves the Experiment object from the persistence store. |
FactorValueData[] |
getFactorValues(long experimentalFactorId)
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HybridizationFileUploadData |
getHybridizationFileUpload(long hybUploadId)
Deprecated. This method is replaced by FileUploadManagerEJB.addHybridizationFileUploadEntry |
HybridizationFileUploadData[] |
getHybridizationFileUploads(long experimentId)
Deprecated. This method is replaced by FileUploadManagerEJB.getHybridizationFileUploadEntries |
HybridizationFileUploadData[] |
getHybridizationFileUploads(long[] hybUploadIds)
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java.lang.String |
getInputFilesDirectory()
Gets the directory for uploading Experiment MAGEML's to. |
java.lang.String |
getInputFilesDirectory(long experimentId)
Deprecated. need to sraigten backend. Move files from ftp area to common area and download from there |
FileData |
getLatestMAGEML(long experimentId)
Gets the information about the latest caARRAY-generated MAGEML for the specified experiment. |
ExperimentCleaningConfiguration |
loadInformation(ExperimentCleaningConfiguration configuration)
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boolean |
lockExperiment(long experimentId)
Locks a particular experiment by changing the visibility to public and relinquishing ownership. |
ExperimentDesc[] |
searchExperiments(ExperimentSearchCriteria criteria)
Searches Experiments |
ExperimentDesc[] |
searchExperiments(ExperimentSearchCriteria criteria,
int pageSize,
int pageNum)
Searches Experiments pagesize 0 imples return averything. |
void |
submitHybridizationFileUploadsForParsing(long experimentId,
long[] hybFileUploadIds)
Deprecated. This functionality is handled by FileUploadManagerEJB for 1.3 |
void |
submitMAGEMLFile(java.lang.String magemlPathName)
This method puts the specified zip file which is residing on the caARRAY server on the queue for the parsing and storing process of MAGEML's. |
void |
submitMAGEMLGeneration(long experimentId)
Submits a MAGEML generation message to the responsible Message Driven Bean to generate MAGEML for the specified experiment. |
void |
updateAdditionalQualifier(long experimentId,
AdditionalQualifierData qualifier)
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long |
updateExperiment(ExperimentData experimentData)
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void |
updateExperimentalFactor(long experimentId,
ExperimentalFactorData factor)
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void |
updateExperimentalFactors(long experimentId,
ExperimentalFactorData[] factorData)
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void |
updateHybridizationFileUpload(HybridizationFileUploadData uploadData)
Deprecated. This method is replaced by FileUploadManagerEJB.addHybridizationFileUploadGroup |
void |
updateProtocolApplication(ProtocolApplicationData pData)
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void |
updatePublication(long experimentId,
PublicationData pubData)
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void |
updateQualityControl(long experimentId,
QualityControlData qualityControlData)
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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 ExperimentManagerEJB()
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 long addExperiment(ExperimentData experimentData, ExperimentalFactorData[] factors) throws java.lang.Exception
experimentData
- - The experiment to be addedfactors
- - An array of factors that are to be added and associated
with the specified experiment. If NULL is provided, it's ignored.
java.lang.Exception
public long updateExperiment(ExperimentData experimentData) throws java.lang.Exception
java.lang.Exception
public void deleteExperiment(long experimentId) throws java.lang.Exception
java.lang.Exception
public long addPublication(long experimentId, PublicationData pubData) throws java.lang.Exception
java.lang.Exception
public void updatePublication(long experimentId, PublicationData pubData) throws java.lang.Exception
java.lang.Exception
public void deletePublicationFromExperiment(long experimentId, long pubId) throws java.lang.Exception
java.lang.Exception
public long addHybridizationFileUpload(long experimentId, HybridizationFileUploadData uploadData) throws java.lang.Exception
HybridizationFileUploadData
are uploaded to the caARRAY server.
This method adds the experiment data contained in the object and then
sends the uploaded hybridization files to the parsing service for
parsing and storing the hybridization data.
java.lang.Exception
public HybridizationFileUploadData[] addHybridizationFileUploads(long experimentId, HybridizationFileUploadData[] uploadData) throws java.lang.Exception
HybridizationFileUploadData
are uploaded to the caARRAY server.
This method adds the experiment data contained in the object and then
sends the uploaded hybridization files to the parsing service for
parsing and storing the hybridization data.
java.lang.Exception
public void updateHybridizationFileUpload(HybridizationFileUploadData uploadData) throws java.lang.Exception
java.lang.Exception
public void deleteHybridizationFileUploadFromExperiment(long experimentId, long id) throws java.lang.Exception
java.lang.Exception
public HybridizationFileUploadData[] getHybridizationFileUploads(long experimentId) throws java.lang.Exception
java.lang.Exception
public HybridizationFileUploadData getHybridizationFileUpload(long hybUploadId) throws java.lang.Exception
java.lang.Exception
public HybridizationFileUploadData[] getHybridizationFileUploads(long[] hybUploadIds) throws java.lang.Exception
java.lang.Exception
public ExperimentDesc[] searchExperiments(ExperimentSearchCriteria criteria) throws java.lang.Exception
java.lang.Exception
public ExperimentDesc[] searchExperiments(ExperimentSearchCriteria criteria, int pageSize, int pageNum) throws java.lang.Exception
java.lang.Exception
public void addAdditionalQualifier(long experimentId, AdditionalQualifierData qualifier) throws java.lang.Exception
java.lang.Exception
public void updateAdditionalQualifier(long experimentId, AdditionalQualifierData qualifier) throws java.lang.Exception
java.lang.Exception
public void deleteAdditionalQualifierFromExperiment(long experimentId, long id) throws java.lang.Exception
java.lang.Exception
public void addExperimentalFactors(long experimentId, ExperimentalFactorData[] factorData) throws java.lang.Exception
java.lang.Exception
public ExperimentalFactorData[] getExperimentalFactors(long experimentId) throws java.lang.Exception
java.lang.Exception
public void updateExperimentalFactor(long experimentId, ExperimentalFactorData factor) throws java.lang.Exception
java.lang.Exception
public void updateExperimentalFactors(long experimentId, ExperimentalFactorData[] factorData) throws java.lang.Exception
java.lang.Exception
public void deleteExperimentalFactorFromExperiment(long experimentId, long id) throws java.lang.Exception
java.lang.Exception
public FactorValueData[] getFactorValues(long experimentalFactorId) throws java.lang.Exception
java.lang.Exception
public long addFactorValue(long experimentalFactorId, FactorValueData valueData) throws java.lang.Exception
java.lang.Exception
public void deleteFactorValueFromExperimentalFactor(long experimentalFactorId, long factorValueId) throws java.lang.Exception
java.lang.Exception
public void addQualityControl(long experimentId, QualityControlData qualityControlData) throws java.lang.Exception
java.lang.Exception
public void updateQualityControl(long experimentId, QualityControlData qualityControlData) throws java.lang.Exception
java.lang.Exception
public void deleteQualityControlFromExperiment(long experimentId, long id) throws java.lang.Exception
java.lang.Exception
public ExperimentView getExperimentView(long id) throws java.lang.Exception
Experiment
object from the persistence store.
ExperimentData
object which ID matches the
specified ID or null otherwise.
java.lang.Exception
public ExperimentData getExperiment(long id) throws java.lang.Exception
Experiment
object from the persistence store.
ExperimentData
object which ID matches the
specified ID or null otherwise.
java.lang.Exception
public void addAdditionalDataProcessing(long experimentId, AdditionalDataProcessingData addDataProcessing) throws java.lang.Exception
java.lang.Exception
public void deleteAdditionalDataProcessingFromExperiment(long experimentId, long id) throws java.lang.Exception
java.lang.Exception
public void addAdditionalUploadedFile(long experimentId, AdditionalUploadedFileData uploadData) throws java.lang.Exception
java.lang.Exception
public void deleteAdditionalUploadedFileFromExperiment(long experimentId, long id) throws java.lang.Exception
java.lang.Exception
public AdditionalDataProcessingData getAdditionalDataProcessing(long id) throws java.lang.Exception
AdditionalDataProcessingData
object from the persistence store.
AdditionalDataProcessingData
object that has
the specified ID.
java.lang.Exception
public AdditionalDataProcessingData[] getAdditionalDataProcessings(long experimentId) throws java.lang.Exception
AdditionalDataProcessingData
object from the persistence store.
AdditionalDataProcessingData
object whose experiment
ID matches the specified ID or null otherwise.
java.lang.Exception
public AdditionalUploadedFileData[] getAdditionalUploadedFiles(long experimentId) throws java.lang.Exception
AdditionalDataProcessingData
object from the persistence store.
AdditionalDataProcessingData
object whose experiment
ID matches the specified ID or null otherwise.
java.lang.Exception
public AdditionalUploadedFileData getAdditionalUploadedFile(long id) throws java.lang.Exception
AdditionalDataProcessingData
object from the persistence store.
AdditionalDataProcessingData
object whose ID
ID matches the specified ID or null otherwise.
java.lang.Exception
public void submitHybridizationFileUploadsForParsing(long experimentId, long[] hybFileUploadIds) throws java.lang.Exception
HybridizationFileUpload
on the queue for the parsing process
to parse, store and associate the data with the specified experiment.
java.lang.Exception
public java.lang.String getInputFilesDirectory() throws java.lang.Exception
java.lang.Exception
public void submitMAGEMLFile(java.lang.String magemlPathName) throws java.lang.Exception
magemlPathName
- - The path on the caARRAY server where the MAGEML
file has been uploaded to.
java.lang.Exception
public java.lang.String getDataFilesDirectory(long experimentId) throws java.lang.Exception
experimentId
- - The experiment for which the returned directory is
intended.
java.lang.Exception
public java.lang.String getInputFilesDirectory(long experimentId) throws java.lang.Exception
experimentId
- - The experiment for which the returned directory is
intended.local
- - true if debugging on local machine
java.lang.Exception
public FileData getLatestMAGEML(long experimentId) throws java.lang.Exception
experimentId
- - The experiment for which the MAGEML is available.
ExperimentMAGEMLData
object containing information
about the latest generated MAGEML or NULL if the experiment does NOT
have the MAGEML generated.
java.lang.Exception
public void submitMAGEMLGeneration(long experimentId) throws java.lang.Exception
java.lang.Exception
public boolean lockExperiment(long experimentId) throws java.lang.Exception
AdditionalDataProcessingData
object whose experiment
ID matches the specified ID or null otherwise.
java.lang.Exception
public boolean checkBatchDownloadFile(long experimentId, java.lang.String fileExtension) throws java.lang.Exception
experimentID
- - The experiment the user is working on
ObjectNotExistException
java.lang.Exception
public void updateProtocolApplication(ProtocolApplicationData pData) throws java.lang.Exception
java.lang.Exception
public ExperimentCleaningConfiguration loadInformation(ExperimentCleaningConfiguration configuration) throws java.lang.Exception
java.lang.Exception
public ExperimentDeletionResult deleteExperiment(ExperimentData experimentData) throws java.lang.Exception
java.lang.Exception
public HybridizationDeletionResult deleteHybridizations(HybridizationDeletionConfiguration configuration) throws java.lang.Exception
java.lang.Exception
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