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java.lang.Objectgov.nih.nci.caarray.services.util.db.ManagerDB
gov.nih.nci.caarray.services.arraydesign.ArrayDesignManagerDB
public final class ArrayDesignManagerDB
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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ArrayDesignManagerDB()
Default Constructor |
Method Summary | |
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long |
addArrayDesign(PhysicalArrayDesign arrayDesign)
Adds the specified ArrayDesign to the persistence store |
void |
addCompositeGroup(long arrayDesignId,
long compositeGroupId)
Add the specified CompositeGroup to the specified
ArrayDesign . |
void |
addCompositeSequence(CompositeGroup compositeGroup,
CompositeSequence compositeSequence)
|
void |
addDesignProviderRole(long arrayDesignId,
DesignProviderRole designProviderRole)
Associate specified provider that has a role with the specified array design |
void |
addFeatureGroup(long arrayDesignId,
long featureGroupId)
Add the specified FeatureGroup to the specified
ArrayDesign . |
long |
addProtocolApplication(long arrayDesignId,
ProtocolApplication protApp)
|
void |
addReporterGroup(long arrayDesignId,
long reporterGroupId)
Add the specified ReporterGroup to the specified
ArrayDesign . |
void |
close()
Close database connection. |
void |
deleteArrayDesign(long arrayDesignId)
Attempts to physically delete the specified ArrayDesign if it contains no Features, Reporters and CompositeSequences. |
void |
deletePotocolApplicationFromArrayDesign(long arrayDesignId,
long protAppId)
|
void |
disableIndexesAndConstraints()
|
void |
enableIndexesAndConstraints()
|
PhysicalArrayDesign |
getArrayDesign(long id)
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PhysicalArrayDesign |
getArrayDesign(java.lang.String identifier)
|
ArrayDesignFileUploadEntry |
getArrayDesignFileUploadEntry(PhysicalArrayDesign design)
|
PhysicalArrayDesign[] |
getArrayDesigns(ArrayDesignSearchCriteria searchCriteria)
Get an array of ArrayDesign that match the specified
Criteria and that the array design is NOT marked as deleted. |
ArrayDesignUploadedFileData |
getArrayDesignUploadedFileData(long id)
|
java.sql.Connection |
getConnection()
|
boolean |
isArrayDesignProvidedByAffymetrix(long id)
|
void |
removeCompositeGroup(long arrayDesignId,
long compositeGroupId)
Remove the specified CompositeGroup from the specified
ArrayDesign . |
void |
removeDesignProvider(long arrayDesignId,
long providerId)
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void |
removeExistingDesignElements(PhysicalArrayDesign arrayDesign)
|
void |
removeFeatureGroup(long arrayDesignId,
long featureGroupId)
Remove the specified FeatureGroup from the specified
ArrayDesign . |
void |
removeReporterGroup(long arrayDesignId,
long reporterGroupId)
Remove the specified ReporterGroup from the specified
ArrayDesign . |
void |
saveArrayDesign(PhysicalArrayDesign arrayDesign)
Alternate (to addArrayDesign) method for saving an array design -- assumes that the associated OntologyEntries are correct and stores all associated objects automatically. |
DesignElementRetrievalSettings |
setEfficientDesignElementRetrieval()
|
void |
setNormalDesignElementRetrieval(DesignElementRetrievalSettings originalSettings)
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void |
updateArrayDesign(PhysicalArrayDesign arrayDesign)
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void |
updateTopLevelOnly(PhysicalArrayDesign arrayDesign)
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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 ArrayDesignManagerDB()
Method Detail |
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public long addArrayDesign(PhysicalArrayDesign arrayDesign) throws java.lang.Exception
ArrayDesign
to the persistence store
ObjectNotExistException
- - When the associated substrate type,
technology type, strand type, attachment type and species are not
existing OntologyEntry
.
InsertObjectException
- - For any reasons, the array design
cannot be inserted.
java.lang.Exception
public void updateArrayDesign(PhysicalArrayDesign arrayDesign) throws java.lang.Exception
java.lang.Exception
public ArrayDesignUploadedFileData getArrayDesignUploadedFileData(long id) throws java.lang.Exception
java.lang.Exception
public void deleteArrayDesign(long arrayDesignId) throws java.lang.Exception
arrayDesignId
-
ObjectNotExistException
ObjectInUseException
DBException
java.lang.Exception
public PhysicalArrayDesign getArrayDesign(java.lang.String identifier) throws java.lang.Exception
java.lang.Exception
public PhysicalArrayDesign getArrayDesign(long id) throws java.lang.Exception
java.lang.Exception
public boolean isArrayDesignProvidedByAffymetrix(long id) throws java.lang.Exception
java.lang.Exception
public PhysicalArrayDesign[] getArrayDesigns(ArrayDesignSearchCriteria searchCriteria) throws java.lang.Exception
ArrayDesign
that match the specified
Criteria
and that the array design is NOT marked as deleted.
criteria
- - An ArrayDesignSearchCriteria
that specifies
the criteria for ArrayDesign
to be searched.
ArrayDesign
if there's at least
one match or a zero-length array otherwise.
java.lang.Exception
public void addDesignProviderRole(long arrayDesignId, DesignProviderRole designProviderRole) throws java.lang.Exception
arrayDesignId
- designProviderRole
- - An association object that associates a
provider with an array design.
java.lang.Exception
public void removeDesignProvider(long arrayDesignId, long providerId) throws java.lang.Exception
arrayDesignId
- providerId
-
java.lang.Exception
public long addProtocolApplication(long arrayDesignId, ProtocolApplication protApp) throws java.lang.Exception
java.lang.Exception
public void deletePotocolApplicationFromArrayDesign(long arrayDesignId, long protAppId) throws java.lang.Exception
java.lang.Exception
public void addCompositeGroup(long arrayDesignId, long compositeGroupId) throws java.lang.Exception
CompositeGroup
to the specified
ArrayDesign
.
arraydesignId
- - The ID of the ArrayDesign
to add the
CompositeGroup
to.hardwareId
- - The ID of the CompositeGroup
to add to the
ArrayDesign
.
ObjectNotExistException
- - If either the ArrayDesign
or CompositeGroup
does not exist.
GeneralException
- -
java.lang.Exception
public void removeCompositeGroup(long arrayDesignId, long compositeGroupId) throws java.lang.Exception
CompositeGroup
from the specified
ArrayDesign
.
arrayDesignId
- - The ID of the ArrayDesign
to remove the
CompositeGroup
from.compositeGroupId
- - The ID of the CompositeGroup
to remove from the
ArrayDesign
.
ObjectNotExistException
- - If either the ArrayDesign
or CompositeGroup
does not exist.
GeneralException
- -
java.lang.Exception
public void addFeatureGroup(long arrayDesignId, long featureGroupId) throws java.lang.Exception
FeatureGroup
to the specified
ArrayDesign
.
arraydesignId
- - The ID of the ArrayDesign
to add the
FeatureGroup
to.hardwareId
- - The ID of the FeatureGroup
to add to the
ArrayDesign
.
ObjectNotExistException
- - If either the ArrayDesign
or FeatureGroup
does not exist.
GeneralException
- -
java.lang.Exception
public void removeFeatureGroup(long arrayDesignId, long featureGroupId) throws java.lang.Exception
FeatureGroup
from the specified
ArrayDesign
.
arrayDesignId
- - The ID of the ArrayDesign
to remove the
FeatureGroup
from.featureGroupId
- - The ID of the FeatureGroup
to remove from the
ArrayDesign
.
ObjectNotExistException
- - If either the ArrayDesign
or FeatureGroup
does not exist.
GeneralException
- -
java.lang.Exception
public void addReporterGroup(long arrayDesignId, long reporterGroupId) throws java.lang.Exception
ReporterGroup
to the specified
ArrayDesign
.
arraydesignId
- - The ID of the ArrayDesign
to add the
ReporterGroup
to.hardwareId
- - The ID of the ReporterGroup
to add to the
ArrayDesign
.
ObjectNotExistException
- - If either the ArrayDesign
or ReporterGroup
does not exist.
GeneralException
- -
java.lang.Exception
public void removeReporterGroup(long arrayDesignId, long reporterGroupId) throws java.lang.Exception
ReporterGroup
from the specified
ArrayDesign
.
arrayDesignId
- - The ID of the ArrayDesign
to remove the
ReporterGroup
from.reporterGroupId
- - The ID of the ReporterGroup
to remove from the
ArrayDesign
.
ObjectNotExistException
- - If either the ArrayDesign
or ReporterGroup
does not exist.
GeneralException
- -
java.lang.Exception
public void close()
ManagerDB
close
in class ManagerDB
public void saveArrayDesign(PhysicalArrayDesign arrayDesign) throws java.lang.Exception
arrayDesign
-
java.lang.Exception
public ArrayDesignFileUploadEntry getArrayDesignFileUploadEntry(PhysicalArrayDesign design) throws java.lang.Exception
java.lang.Exception
public void removeExistingDesignElements(PhysicalArrayDesign arrayDesign) throws java.lang.Exception
arrayDesign
-
java.lang.Exception
public void disableIndexesAndConstraints() throws org.apache.ojb.broker.accesslayer.LookupException, java.sql.SQLException
org.apache.ojb.broker.accesslayer.LookupException
java.sql.SQLException
public void enableIndexesAndConstraints() throws org.apache.ojb.broker.accesslayer.LookupException, java.sql.SQLException
org.apache.ojb.broker.accesslayer.LookupException
java.sql.SQLException
public DesignElementRetrievalSettings setEfficientDesignElementRetrieval()
public void setNormalDesignElementRetrieval(DesignElementRetrievalSettings originalSettings)
public void updateTopLevelOnly(PhysicalArrayDesign arrayDesign) throws java.lang.Exception
java.lang.Exception
public java.sql.Connection getConnection() throws org.apache.ojb.broker.accesslayer.LookupException
org.apache.ojb.broker.accesslayer.LookupException
public void addCompositeSequence(CompositeGroup compositeGroup, CompositeSequence compositeSequence)
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