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java.lang.Objectgov.nih.nci.caarray.services.util.db.ManagerDB
gov.nih.nci.caarray.services.experiment.ExperimentManagerDB
public final class ExperimentManagerDB
Field Summary |
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Fields inherited from class gov.nih.nci.caarray.services.util.db.ManagerDB |
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CASCADE_LINK, CASCADE_NONE, CASCADE_OBJECT, ID_UNSET |
Constructor Summary | |
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ExperimentManagerDB()
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Method Summary | |
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long |
addAdditionalDataProcessing(long experimentId,
AdditionalDataProcessing additionalProcessing)
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long |
addAdditionalQualifier(long experimentId,
OntologyEntry qualifier)
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long |
addAdditionalUploadedFile(long experimentId,
AdditionalUploadedFile additionalUploadedFile)
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long |
addBibliographicReference(long experimentId,
BibliographicReference bf)
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long |
addExperiment(Experiment experiment)
Add the specified Experiment to the persistence store |
long |
addExperimentalFactor(long experimentId,
ExperimentalFactor factor)
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void |
addExperimentalFactors(long experimentId,
ExperimentalFactor[] factors)
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long |
addFactorValue(long experimentalFactorId,
FactorValue value)
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void |
addFactorValues(long experimentalFactorId,
FactorValue[] values)
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long |
addHybridizationFileUpload(long experimentId,
HybridizationFileUpload hybUpload)
This method performs the following: Add caARRAY-specific HybridizationFileUpload
to the persistence store. |
long[] |
addHybridizationFileUploads(long experimentId,
HybridizationFileUpload[] hybUploads)
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long |
addQualityControl(long experimentId,
Description qualityControl)
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void |
close()
Close database connection. |
void |
convertFactorValueMeasurementsToValues(Experiment exp)
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int |
countHybridizationFileUploadEntries(long experimentId)
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int |
countHybridizationFileUploads(long experimentId)
Deprecated. This method was replaced by countHybridizationFileUploadEntries for the redesigned |
void |
deleteAdditionalDataProcessing(long experimentId,
long additionalDataProcessingId)
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void |
deleteAdditionalQualifier(long experimentId,
long qualifierId)
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void |
deleteAdditionalUploadedFile(long experimentId,
long additionalUploadedFileId)
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void |
deleteBibliographicReferenceFromExperiment(long experimentId,
long bfId)
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boolean |
deleteBioAssayFromExperiment(BioAssay bioAssay,
Experiment experiment)
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void |
deleteExperiment(long experimentId)
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void |
deleteExperimentalFactorFromExperiment(long experimentId,
long factorId)
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void |
deleteFactorValueFromExperimentalFactor(long experimentalFactorId,
long valueId)
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void |
deleteHybridizationFileUploadEntryFromExperiment(long experimentId,
long id)
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void |
deleteHybridizationFileUploadFromExperiment(long experimentId,
long id)
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void |
deleteQualityControlFromExperiment(long experimentId,
long qualityControlId)
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AdditionalDataProcessing |
getAdditionalDataProcessing(long addDataProcessingId)
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AdditionalDataProcessing[] |
getAdditionalDataProcessings(long experimentId)
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OntologyEntry |
getAdditionalQualifier(long id)
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AdditionalUploadedFile |
getAdditionalUploadedFile(long uploadedFileId)
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AdditionalUploadedFile[] |
getAdditionalUploadedFiles(long experimentId)
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Array |
getArray(long id)
This method returns a Array that has the specified
ID by delegating the call to the same method in ArrayManagerDB . |
PhysicalArrayDesign |
getArrayDesign(long id)
This method returns a PhysicalArrayDesign that has the specified
ID by delegating the call to the same method in ArrayDesignManagerDB . |
BibliographicReference |
getBibliographicReference(long id)
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Experiment |
getExperiment(long id)
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ExperimentalFactor |
getExperimentalFactor(long id)
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ExperimentalFactor[] |
getExperimentalFactors(long experimentId)
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java.util.Date |
getExperimentDate(long experimentId)
Workaround for efficiency to get the date for experiment fast. |
Experiment[] |
getExperiments(ExperimentSearchCriteria criteria)
Gets Experiments. |
Experiment[] |
getExperimentsReferencingArrayGroup(long arrayGroupId)
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FactorValue[] |
getFactorValues(long experimentalFactorId)
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HybridizationFileUpload |
getHybridizationFileUpload(long hybUploadId)
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HybridizationFileUpload[] |
getHybridizationFileUploads(long experimentId)
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HybridizationFileUpload[] |
getHybridizationFileUploads(long[] hybUploadIds)
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Protocol |
getProtocol(long id)
This method returns a Protocol that has the specified ID by
delegating the call to the same method in ProtocolManagerDB . |
Description |
getQualityControlDescription(long id)
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void |
updateAdditionalQualifier(OntologyEntry qualifier)
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void |
updateBibliographicReference(BibliographicReference bf)
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void |
updateExperiment(Experiment experiment)
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void |
updateExperimentalFactor(ExperimentalFactor factor)
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void |
updateHybridizationFileUpload(HybridizationFileUpload hybUpload)
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void |
updateProtocolApplication(ProtocolApplicationData paData)
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void |
updateQualityControl(Description qualityControl)
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Methods inherited from class gov.nih.nci.caarray.services.util.db.ManagerDB |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ExperimentManagerDB()
Method Detail |
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public Experiment getExperiment(long id) throws java.lang.Exception
id
-
ObjectNotExistException
DBException
java.lang.Exception
public long addExperiment(Experiment experiment) throws java.lang.Exception
Experiment
to the persistence store
java.lang.Exception
public void updateExperiment(Experiment experiment) throws java.lang.Exception
java.lang.Exception
public BibliographicReference getBibliographicReference(long id) throws java.lang.Exception
java.lang.Exception
public long addBibliographicReference(long experimentId, BibliographicReference bf) throws java.lang.Exception
java.lang.Exception
public void updateBibliographicReference(BibliographicReference bf) throws java.lang.Exception
java.lang.Exception
public void deleteBibliographicReferenceFromExperiment(long experimentId, long bfId) throws java.lang.Exception
id
-
ObjectNotExistException
DBException
java.lang.Exception
public long addAdditionalQualifier(long experimentId, OntologyEntry qualifier) throws java.lang.Exception
experimentId
- qualifier
-
ObjectNotExistException
InsertObjectException
DBException
java.lang.Exception
public void updateAdditionalQualifier(OntologyEntry qualifier) throws java.lang.Exception
qualifier
-
ObjectNotExistException
DBException
java.lang.Exception
public long addExperimentalFactor(long experimentId, ExperimentalFactor factor) throws java.lang.Exception
java.lang.Exception
public void addExperimentalFactors(long experimentId, ExperimentalFactor[] factors) throws java.lang.Exception
java.lang.Exception
public long addFactorValue(long experimentalFactorId, FactorValue value) throws java.lang.Exception
java.lang.Exception
public void addFactorValues(long experimentalFactorId, FactorValue[] values) throws java.lang.Exception
java.lang.Exception
public void convertFactorValueMeasurementsToValues(Experiment exp)
public FactorValue[] getFactorValues(long experimentalFactorId) throws java.lang.Exception
java.lang.Exception
public void updateProtocolApplication(ProtocolApplicationData paData) throws java.lang.Exception
java.lang.Exception
public void deleteFactorValueFromExperimentalFactor(long experimentalFactorId, long valueId) throws java.lang.Exception
java.lang.Exception
public OntologyEntry getAdditionalQualifier(long id) throws java.lang.Exception
java.lang.Exception
public ExperimentalFactor getExperimentalFactor(long id) throws java.lang.Exception
java.lang.Exception
public ExperimentalFactor[] getExperimentalFactors(long experimentId) throws java.lang.Exception
java.lang.Exception
public void updateExperimentalFactor(ExperimentalFactor factor) throws java.lang.Exception
java.lang.Exception
public void deleteExperimentalFactorFromExperiment(long experimentId, long factorId) throws java.lang.Exception
experimentId
- factorId
-
ObjectNotExistException
DBException
java.lang.Exception
public void deleteExperiment(long experimentId) throws java.lang.Exception
id
-
ObjectNotExistException
DBException
java.lang.Exception
public void deleteAdditionalQualifier(long experimentId, long qualifierId) throws java.lang.Exception
id
-
ObjectNotExistException
DBException
java.lang.Exception
public Experiment[] getExperiments(ExperimentSearchCriteria criteria)
public Description getQualityControlDescription(long id) throws java.lang.Exception
java.lang.Exception
public long addQualityControl(long experimentId, Description qualityControl) throws java.lang.Exception
java.lang.Exception
public void updateQualityControl(Description qualityControl) throws java.lang.Exception
java.lang.Exception
public void deleteQualityControlFromExperiment(long experimentId, long qualityControlId) throws java.lang.Exception
id
-
ObjectNotExistException
DBException
java.lang.Exception
public long addAdditionalDataProcessing(long experimentId, AdditionalDataProcessing additionalProcessing) throws java.lang.Exception
java.lang.Exception
public long addAdditionalUploadedFile(long experimentId, AdditionalUploadedFile additionalUploadedFile) throws java.lang.Exception
java.lang.Exception
public void deleteAdditionalDataProcessing(long experimentId, long additionalDataProcessingId) throws java.lang.Exception
java.lang.Exception
public void deleteAdditionalUploadedFile(long experimentId, long additionalUploadedFileId) throws java.lang.Exception
java.lang.Exception
public AdditionalDataProcessing getAdditionalDataProcessing(long addDataProcessingId) throws java.lang.Exception
java.lang.Exception
public AdditionalDataProcessing[] getAdditionalDataProcessings(long experimentId) throws java.lang.Exception
java.lang.Exception
public AdditionalUploadedFile getAdditionalUploadedFile(long uploadedFileId) throws java.lang.Exception
java.lang.Exception
public AdditionalUploadedFile[] getAdditionalUploadedFiles(long experimentId) throws java.lang.Exception
java.lang.Exception
public HybridizationFileUpload getHybridizationFileUpload(long hybUploadId) throws java.lang.Exception
java.lang.Exception
public HybridizationFileUpload[] getHybridizationFileUploads(long[] hybUploadIds) throws java.lang.Exception
java.lang.Exception
public int countHybridizationFileUploads(long experimentId) throws java.lang.Exception
experimentId
-
DBException
java.lang.Exception
public int countHybridizationFileUploadEntries(long experimentId) throws java.lang.Exception
java.lang.Exception
public java.util.Date getExperimentDate(long experimentId) throws java.lang.Exception
java.lang.Exception
public HybridizationFileUpload[] getHybridizationFileUploads(long experimentId) throws java.lang.Exception
java.lang.Exception
public long addHybridizationFileUpload(long experimentId, HybridizationFileUpload hybUpload) throws java.lang.Exception
HybridizationFileUpload
to the persistence store.
MeasuredBioAssay
object contained in
the specified HybridizationFileUpload
with the specified
Experiment
.
DerivedBioAssay
object for later contain
the hydization data parsed by a different process and associate the object
with the specified Experiment
.
experimentId
- upload
-
ObjectNotExistException
InsertObjectException
DBException
java.lang.Exception
public long[] addHybridizationFileUploads(long experimentId, HybridizationFileUpload[] hybUploads) throws java.lang.Exception
java.lang.Exception
public void updateHybridizationFileUpload(HybridizationFileUpload hybUpload) throws java.lang.Exception
java.lang.Exception
public void deleteHybridizationFileUploadFromExperiment(long experimentId, long id) throws java.lang.Exception
java.lang.Exception
public void deleteHybridizationFileUploadEntryFromExperiment(long experimentId, long id) throws java.lang.Exception
java.lang.Exception
public Protocol getProtocol(long id) throws java.lang.Exception
Protocol
that has the specified ID by
delegating the call to the same method in ProtocolManagerDB
.
This allows ExperimentManagerEJB
to interface with a single
ManagerDB
.
id
-
java.lang.Exception
public PhysicalArrayDesign getArrayDesign(long id) throws java.lang.Exception
PhysicalArrayDesign
that has the specified
ID by delegating the call to the same method in ArrayDesignManagerDB
.
This allows ExperimentManagerEJB
to interface with a single
ManagerDB
.
id
-
java.lang.Exception
public Array getArray(long id) throws java.lang.Exception
Array
that has the specified
ID by delegating the call to the same method in ArrayManagerDB
.
id
-
java.lang.Exception
public Experiment[] getExperimentsReferencingArrayGroup(long arrayGroupId) throws java.lang.Exception
java.lang.Exception
public boolean deleteBioAssayFromExperiment(BioAssay bioAssay, Experiment experiment) throws java.lang.Exception
java.lang.Exception
public void close()
ManagerDB
close
in class ManagerDB
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