org.sigpath.task
Class DBTask

java.lang.Object
  org.sigpath.task.DBTask

All Implemented Interfaces:

Task

Direct Known Subclasses:

SampleReviewData, TAddAlias, TAddChemicals, TAddConcentration, TAddModel, TAddPathway, TAddReactions, TCheckDBAlive, TCheckDeletePermission, TConfirmComponent, TConfirmReactions, TConvertChemical, TConvertSPIDsToBIDs, TConvertVMaxToKp, TCreateExternalReference, TCreateNewPendingList, TDeleteAlias, TDeleteExternalReference, TEditAlias, TEditExternalReference, TEditSigPathEntity, TExportBase, TExportModel, TExportModelReactionsFromSpids, TExportModifiedEntities, TGetAllPendingLists, TGetChemical, TGetConcentrations, TGetConcentrationsByReaction, TGetDBInfo, TGetFilteredUnitsNames, TGetKineticNames, TGetModel, TGetMoleculesFromReactions, TGetOrganismNames, TGetPathway, TGetPendingList, TGetRemoteSpidRange, TGetSigPathEntity, TGetSpidByDbAc, TGetSpidRange, TGetUsers, TGetXMLBindingsFromKinetic, TGetXMLKinetic, TImportBase, TImportModifiedEntities, TIndexModifiedChemicals, TLinkComponentsToReactions, TMarkSpidRange, TOrganismOptimizer, TPopulateBackwardReferences, TPopulateSigPathEntitySummary, TRemoveConcentration, TRemoveSigPathEntity, TSaveConcMeasurements, TSaveNamedChemicals, TSavePendingReviews, TSaveProteins, TSaveSmallMolecules, TScanEnzReactionsAndReactions, TSearchMolecules, TSearchTask, TUpdatePendingList, TUpdateSpidRange, TValidateSPE, TViewImage, TViewImageNone, TViewImageYFiles

public abstract class DBTask
extends Object
implements Task

Specifies a single atomic database operation. DBTask centralizes all transactions, logging, monitoring, and exception handling in one place. This frees the subclasses to focus on business logic.

Author:

Ethan Cerami

Field Summary

protected SPDBManager	dbManager The SigPath Database Manager.
protected boolean	embeddedTask Flag to denote embedded Tasks.
protected EntityManager	entityManager The SigPath Entity Manager.
protected ValidationErrors	errors Validation Errors for this task.
protected FullTextSearchManager	ftsm The SigPath FullTextSearchManager.
protected ProgressListener	progressListener ProgressListener for Monitoring Tasks.
protected SigPathFactory	sigpathFactory The SigPath factory.
protected UnitManager	unitManager The SigPath Unit Manager.
protected UserManager	userManager The SigPath User Manager.
protected XDebug	xdebug Live XDebug Object.

Constructor Summary

DBTask()
Construct a new DBTask object.

DBTask(ValidationErrors errors)
Construct a new DBTask object.

Method Summary

protected abstract void	_execute() Runs the actual database query(ies)/update(s).
void	close() Closes the dbmanager.
protected void	delete(Object object) Deletes a persistent object from the database.
void	execute(XDebug xd) Executes the database task.
SPDBManager	getDbManager() Gets the database manager associated with this task.
ValidationErrors	getErrors() Gets the ValidationErrors object for this task.
boolean	isEmbeddedTask() Determines if this task is embedded or not.
boolean	isTaskThrewException() Did this task's _execute method throw an exception?
protected void	reindex(SigPathEntity spe)
protected void	resolve(Object object) Resolves a persistent object.
void	setDbManager(SPDBManager dbManager) Sets the dbManager to be used for this task.
void	setEmbeddedTask(boolean embeddedTask) Indicate whether or not the task should be embedded.
void	setEmbeddedTask(SPDBManager dbManager) Indicate that the task should be embedded using the specified SPDBManager.
void	setObtainTransactionsFrom(SPDBManager dbManager) Instructs this task to use transactions from a given db manager.
void	setProgressListener(ProgressListener progressListener) Sets the Progress Listener.
protected void	setTaskThrewException(boolean taskThrewException)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

dbManager

protected SPDBManager dbManager

The SigPath Database Manager.

ftsm

protected FullTextSearchManager ftsm

The SigPath FullTextSearchManager.

userManager

protected UserManager userManager

The SigPath User Manager.

entityManager

protected EntityManager entityManager

The SigPath Entity Manager.

sigpathFactory

protected SigPathFactory sigpathFactory

The SigPath factory.

unitManager

protected UnitManager unitManager

The SigPath Unit Manager.

xdebug

protected XDebug xdebug

Live XDebug Object.

embeddedTask

protected boolean embeddedTask

Flag to denote embedded Tasks.

progressListener

protected ProgressListener progressListener

ProgressListener for Monitoring Tasks.

errors

protected ValidationErrors errors

Validation Errors for this task.

Constructor Detail

DBTask

public DBTask()

Construct a new DBTask object.

DBTask

public DBTask(ValidationErrors errors)

Construct a new DBTask object.

Parameters:

errors - ValidationErrors object

Method Detail

getDbManager

public SPDBManager getDbManager()

Gets the database manager associated with this task.

Returns:

setDbManager

public void setDbManager(SPDBManager dbManager)

Sets the dbManager to be used for this task.

Parameters:

dbManager -

setObtainTransactionsFrom

public void setObtainTransactionsFrom(SPDBManager dbManager)

Instructs this task to use transactions from a given db manager. The task thereafter behaves as if it was embedded in another task: it will not begin or commit/abort transactions by itself. Instead, it expects an active transaction when its _execute() method is invoked. Set the database manager to use for this task.

Parameters:

dbManager - Manager of the

isEmbeddedTask

public boolean isEmbeddedTask()

Determines if this task is embedded or not.

Returns:

true if the task is embedded.

setEmbeddedTask

public void setEmbeddedTask(boolean embeddedTask)

Indicate whether or not the task should be embedded. An embedded task will not start a new transaction, but use the current active transaction.

Parameters:

embeddedTask - true if the task should not start a transaction

execute

public void execute(XDebug xd)
             throws SigPathDatabaseException

Executes the database task. If xdebug is set to null, a new XDebug object is automatically created.

Specified by:

execute in interface Task

Parameters:

xd - XDebug object for real-time debugging.

Throws:

SigPathDatabaseException - error connecting to database

isTaskThrewException

public boolean isTaskThrewException()

Did this task's _execute method throw an exception?

Returns:

True if this task _execute method threw an exception, False otherwise.

setTaskThrewException

protected void setTaskThrewException(boolean taskThrewException)

close

public void close()
           throws SigPathDatabaseException

Closes the dbmanager.

Throws:

SigPathDatabaseException

_execute

protected abstract void _execute()
                          throws SigPathDatabaseException

Runs the actual database query(ies)/update(s). Must be implemented by all subclasses.

Throws:

SigPathDatabaseException - error connecting to database

resolve

protected void resolve(Object object)

Resolves a persistent object.

Parameters:

object - Any persistent object

delete

protected void delete(Object object)
               throws SigPathDatabaseException

Deletes a persistent object from the database.

Parameters:

object - Any persistent object

Throws:

SigPathDatabaseException - Indicates Error Connecting to Database

reindex

protected void reindex(SigPathEntity spe)
                throws SigPathDatabaseException

Throws:

SigPathDatabaseException

setEmbeddedTask

public void setEmbeddedTask(SPDBManager dbManager)

Indicate that the task should be embedded using the specified SPDBManager. An embedded task will not start a new transaction, but use the current active transaction. This method should be called every time that a task is embedded in another task. Calling this method guarantees that the tasks operate in the same transaction. This method loads managers for the task, making it safe to use them before execute() is called on the task. This case occurs in the code base, for instance in TExportReaction.

Parameters:

dbManager - Database Manager to use for this task.

setProgressListener

public void setProgressListener(ProgressListener progressListener)

Sets the Progress Listener. Used to monitor long term tasks.

Parameters:

progressListener - Progress Listener Object

getErrors

public ValidationErrors getErrors()

Gets the ValidationErrors object for this task.

Returns:

ValidationErrors object containing errors for this task