org.kepler.provenance.sql

Class SQLRecordingV8

java.lang.Object

org.kepler.provenance.Recording

org.kepler.provenance.sql.SQLRecording

org.kepler.provenance.sql.SQLRecordingV7

org.kepler.provenance.sql.SQLRecordingV8

public class SQLRecordingV8
extends SQLRecordingV7

SQL provenance output. NOTE: The v8 schema is under development and likely to change. This uses version 8 of the schema. New features:

• Saving the workflow contents for each execution.
• Saving contents of files referenced in tokens.
• Each workflow and workflow execution has unique LSID.
• Workflow name no longer required.
• Explicit mapping from token write to token read.
• Combining actor firing events into a single "firing cycle event".
• Recording execution exceptions.
• Storing associated data for executions.

Author:

Derik Barseghian, Daniel Crawl, Ben Leinfelder, Sean Riddle

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	SQLRecordingV8.SQLRecordingParametersV8 A subclass of SQLRecordingParameters that adds more parameters.
protected static class	SQLRecordingV8.TokenInfo The class used in the port queues to contain the port event write id and data md5.

Nested classes/interfaces inherited from class org.kepler.provenance.sql.SQLRecording

SQLRecording.PortDirection

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	_execAnnotation Value of execution annotation parameter.
protected boolean	_executionHadAnError True if executionError is called
protected java.util.Map<KeplerLSID,java.lang.Integer>	_executionLSIDtoIdMap
protected java.lang.String	_nextExecLSIDStr Value of next execution LSID parameter.
protected PortConnector<SQLRecordingV8.TokenInfo>	_portConnector Class for token dependencies.
protected java.sql.PreparedStatement	_psAssocDataInsert
protected java.sql.PreparedStatement	_psAssocDataInsertNoDataId
protected java.sql.PreparedStatement	_psChangeExecutionLSID
protected java.sql.PreparedStatement	_psChangeExecutionReferralList
protected java.sql.PreparedStatement	_psChangeExecutionType
protected java.sql.PreparedStatement	_psChangeWorkflowName
protected java.sql.PreparedStatement	_psDataInsert
protected java.sql.PreparedStatement	_psDataMD5Query
protected java.sql.PreparedStatement	_psDeleteData
protected java.sql.PreparedStatement	_psDeleteExecutions
protected java.sql.PreparedStatement	_psDeleteTagForExecIdAndURN
protected java.sql.PreparedStatement	_psDeleteTags
protected java.sql.PreparedStatement	_psDeleteWorkflowsForNoExecutions
protected java.sql.PreparedStatement	_psErrorInsert
protected java.sql.PreparedStatement	_psGetAssociatedDataDataIdsToDeleteQuery
protected java.sql.PreparedStatement	_psGetAssociatedDataDataIdsToNotDeleteQuery
protected java.sql.PreparedStatement	_psGetPortEventDataIdsToDeleteQuery
protected java.sql.PreparedStatement	_psGetPortEventDataIdsToNotDeleteQuery
protected java.sql.PreparedStatement	_psGetTagForExecIdAndURN
protected java.sql.PreparedStatement	_psGetWfContentsIdsToDeleteQuery
protected java.sql.PreparedStatement	_psGetWfContentsIdsToNotDeleteQuery
protected java.sql.PreparedStatement	_psParameterExecInsert
protected java.sql.PreparedStatement	_psPortEventInsert
protected java.sql.PreparedStatement	_psPortEventInsertWithChecksum
protected java.sql.PreparedStatement	_psTagInsert
protected java.sql.PreparedStatement	_psWorkflowIdsForNoExecutions
protected Queryable	_queryable Queryable connection.
protected int	_wfLastExecId The most recently completed workflow execution id.
protected KeplerLSID	_wfLSID The current workflow id.
static int	MAX_PORT_EVENT_DATA_LENGTH The maximum length of the data stored in the port_event table.

Fields inherited from class org.kepler.provenance.sql.SQLRecordingV7

_evolId, _psParameterValueQuery, _psWorkflowChangeInsert, _workflowChangeTimeStack

Fields inherited from class org.kepler.provenance.sql.SQLRecording

_dbParams, _dbType, _entityCacheTable, _fireStateTable, _maxDataSize, _maxParameterValueSize, _needReconnectDB, _needReconnectWF, _params, _psActionInsert, _psActorFireStart, _psActorFireStop, _psActorInsert, _psDirectorInsert, _psEntityInsert, _psEntityQuery, _psLinkInsert, _psParameterInsert, _psPortInsert, _psRelationInsert, _psTokenFlowInsert, _psWorkflowExecStart, _psWorkflowExecStop, _psWorkflowInsert, _psWorkflowQuery, _schema, _wfExecId, _wfId, _wfNameStr, _wfUserStr, DATA_NONE, DATA_TRUNCATED, DATA_VALID, SUCCESS, WORKFLOW_ALREADY_EXISTS, WORKFLOW_DOES_NOT_EXIST

Fields inherited from class org.kepler.provenance.Recording

_containerFullName, _containerLSID, _containerName, _debugPrint, _debugWriter, _machineStr, _recorder, _recorderContainer, _stateSerializer

Constructor Summary

Constructors

Constructor and Description
SQLRecordingV8()

Method Summary

Modifier and Type	Method and Description
protected org.kepler.provenance.sql.RegEntity	_addEntity(int containerId, RegEntity.EntityType type, java.lang.String fullName, java.lang.String displayName, int prevId) Add a new row to the entity table.
protected void	_addWorkflow() Add a new row to the workflow table.
protected void	_addWorkflowChange() Create a new row in the workflow_change table.
protected java.lang.String	_changeEntityFullName(java.lang.String name) Modify a NamedObj's full name.
protected void	_changeWorkflowNameColumn(java.lang.String newName) Change the workflow.name column for the current workflow.
protected void	_changeWorkflowNameColumn(java.lang.String newName, KeplerLSID lsid) Change the workflow.name column for a specific LSID.
protected java.lang.String	_checkData(byte[] data) Adds data to the data table if not already there.
protected java.lang.String	_checkData(java.io.File file) Adds data to the data table if not already there.
protected java.lang.String	_checkForFileData(Token token) See if a token contains a valid filename.
protected void	_checkWorkflowName() Check validity of workflow name parameter.
protected void	_createPreparedStatements() Initialize the prepared statements.
protected Schema	_createSchema() Create a Schema to reflect the v8 schema.
protected void	_dbReset() Reset when we use a different db connection.
protected int	_getContainerId(Nameable namedObj) Find the container id of an entity.
protected int	_getMaxTokenDataSize() Get the maximum size of token data that can be stored in the database.
protected int	_getWorkflowId() Get the internal workflow id.
protected void	_nullPreparedStatements() Set our prepared statements to null.
protected void	_reconnectDatabase(boolean resetDB) Reconnect to the database.
protected void	_reconnectWorkflow() Re-acquire the current workflow id.
protected void	_recordActorFireStop(int fireId, Actor actor, java.util.Date timestamp) Record the end of an actor fire and attempt to serialize the actor's state.
protected void	_recordFiringEvent(Actor actor, FiringEvent.FiringEventType type, java.util.Date timestamp) Record a specific type of firing for an actor.
protected void	_recordPortEvent(IOPort port, int fireId, int rwfireId, boolean isRead, int channel, Token token, IOPort destPort, java.util.Date timestamp) Record a specific type of firing for an actor.
protected void	_regPortReal(TypedIOPort port, org.kepler.provenance.sql.RegEntity re) Add a port to the port table.
protected void	_updateParameterExecTable() Add all the parameter ids to the parameter_exec table.
protected void	_wfReset() Reset when we use a different workflow.
void	addFileForExecution(java.util.Map<java.lang.String,java.lang.String> metadataMap, java.io.File file, int execId) Associate the contents of a file with the most recent workflow execution.
void	addFileForLastExecution(java.util.Map<java.lang.String,java.lang.String> metadataMap, java.io.File file) Associate the contents of a file with the most recent workflow execution.
void	attributeChanged(Attribute attribute) React to a change in an attribute.
boolean	changeExecutionLSID(int execId, KeplerLSID newExecLSID, Queryable q) Change execution LSID for an execution Id.
boolean	changeExecutionType(KeplerLSID executionLSID, WorkflowRun.type type) Change the execution type.
boolean	checkIfTagAlreadyInserted(int execId, java.lang.String urn)
void	customProvEvent(ProvenanceEvent event) Record a custom provenance event.
int	deleteExecutions(java.util.List<KeplerLSID> lsidList) Delete executions given a list of execution LSIDs.
int	deleteWorkflowsWithNoExecutions() Delete workflows from the database that have no executions.
void	executionError(Nameable source, java.lang.Throwable throwable, KeplerLSID executionLSID) An actor threw an exception.
void	executionStart(KeplerLSID executionLSID, java.util.Date timestamp) Record the starting of workflow execution.
void	executionStop(KeplerLSID executionLSID, java.util.Date timestamp) Record the stopping of workflow execution.
RecordingParameters	generateParameters(NamedObj no) Add Parameters for ProvenanceRecorder.
Queryable	getQueryable(boolean allowReconnectWF) Get a Queryable connected to the Recording output.
void	insertAnyHuskRunReferralList(WorkflowRun run)
boolean	insertHuskRun(KARFile karFile, WorkflowRun run) If run's exec LSID does not already exist in provenance, insert WorkflowRun into provenance.
boolean	insertPreviewRun(WorkflowRun run) If run's exec LSID does not already exist in provenance, insert WorkflowRun into provenance.
void	insertTag(java.lang.String type, java.lang.String tagStr, java.lang.String urnStr, int execId) Insert a new row into the tag table.
void	insertWorkflowTags(int execId) Parse workflow moml for tags, and insert them, associated with execID
void	refillPortEvent(IOPortRefillEvent event) Record a port refill event.
boolean	regContents() Returns true if workflow contents should be registered.
boolean	regLink(NamedObj endPoint1, NamedObj endPoint2) Register a link between two endpoints.
boolean	regParameter(NamedObj parameter) Register a parameter.
boolean	regPort(TypedIOPort port) Register a port or portparameter.
boolean	regRelation(IORelation relation) Register a relation.
void	renamedWorkflow(NamedObj namedObj, KeplerLSID oldLSID, KeplerLSID newLSID, java.lang.String oldName, java.lang.String newName) A workflow was renamed.
void	tagAdded(TagEvent event) A tag was added, insert it
void	tagRemoved(TagEvent event) A tag was removed.

Methods inherited from class org.kepler.provenance.sql.SQLRecordingV7

_errorReset, _possibleWorkflowChangeStart, _possibleWorkflowChangeStop, evolutionStart, evolutionStop, specificationStart, specificationStop

Methods inherited from class org.kepler.provenance.sql.SQLRecording

_checkConnection, _checkEntity, _checkParameters, _getMaxParameterValueSize, _getWorkflowId, _regActorDirector, _regParameterReal, _updateWorkflowID, actorFire, disconnect, executionImported, executionStart, executionStop, portEvent, regActor, regDirector

Methods inherited from class org.kepler.provenance.Recording

_debug, _debug, _debugWrite, _debugWrite, _error, _getExceptionMessage, _getNameableFullName, _needWorkflowContents, _updateContainerName, _warn, actorFire, executionError, executionImported, executionStart, executionStart, executionStop, executionStop, getContainer, portEvent, remove, removeLink, removeStateSerializer, rename, setContainer, setContainerLSID, setContainerName, setDebugWriter, setStateSerializer

Methods inherited from class java.lang.Object

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

Field Detail

_portConnector

protected PortConnector<SQLRecordingV8.TokenInfo> _portConnector

Class for token dependencies.

_psDataInsert

protected java.sql.PreparedStatement _psDataInsert

_psDataMD5Query

protected java.sql.PreparedStatement _psDataMD5Query

_psPortEventInsert

protected java.sql.PreparedStatement _psPortEventInsert

_psPortEventInsertWithChecksum

protected java.sql.PreparedStatement _psPortEventInsertWithChecksum

_psChangeWorkflowName

protected java.sql.PreparedStatement _psChangeWorkflowName

_psChangeExecutionLSID

protected java.sql.PreparedStatement _psChangeExecutionLSID

_psChangeExecutionReferralList

protected java.sql.PreparedStatement _psChangeExecutionReferralList

_psChangeExecutionType

protected java.sql.PreparedStatement _psChangeExecutionType

_psAssocDataInsert

protected java.sql.PreparedStatement _psAssocDataInsert

_psAssocDataInsertNoDataId

protected java.sql.PreparedStatement _psAssocDataInsertNoDataId

_psErrorInsert

protected java.sql.PreparedStatement _psErrorInsert

_psDeleteExecutions

protected java.sql.PreparedStatement _psDeleteExecutions

_psDeleteData

protected java.sql.PreparedStatement _psDeleteData

_psGetWfContentsIdsToDeleteQuery

protected java.sql.PreparedStatement _psGetWfContentsIdsToDeleteQuery

_psGetWfContentsIdsToNotDeleteQuery

protected java.sql.PreparedStatement _psGetWfContentsIdsToNotDeleteQuery

_psGetAssociatedDataDataIdsToDeleteQuery

protected java.sql.PreparedStatement _psGetAssociatedDataDataIdsToDeleteQuery

_psGetAssociatedDataDataIdsToNotDeleteQuery

protected java.sql.PreparedStatement _psGetAssociatedDataDataIdsToNotDeleteQuery

_psGetPortEventDataIdsToDeleteQuery

protected java.sql.PreparedStatement _psGetPortEventDataIdsToDeleteQuery

_psGetPortEventDataIdsToNotDeleteQuery

protected java.sql.PreparedStatement _psGetPortEventDataIdsToNotDeleteQuery

_psGetTagForExecIdAndURN

protected java.sql.PreparedStatement _psGetTagForExecIdAndURN

_psTagInsert

protected java.sql.PreparedStatement _psTagInsert

_psDeleteTagForExecIdAndURN

protected java.sql.PreparedStatement _psDeleteTagForExecIdAndURN

_psDeleteTags

protected java.sql.PreparedStatement _psDeleteTags

_psParameterExecInsert

protected java.sql.PreparedStatement _psParameterExecInsert

_psDeleteWorkflowsForNoExecutions

protected java.sql.PreparedStatement _psDeleteWorkflowsForNoExecutions

_psWorkflowIdsForNoExecutions

protected java.sql.PreparedStatement _psWorkflowIdsForNoExecutions

_queryable

protected Queryable _queryable

Queryable connection.

_wfLastExecId

protected int _wfLastExecId

The most recently completed workflow execution id.

_execAnnotation

protected java.lang.String _execAnnotation

Value of execution annotation parameter.

_nextExecLSIDStr

protected java.lang.String _nextExecLSIDStr

Value of next execution LSID parameter.

_wfLSID

protected KeplerLSID _wfLSID

The current workflow id.

_executionHadAnError

protected boolean _executionHadAnError

True if executionError is called

_executionLSIDtoIdMap

protected java.util.Map<KeplerLSID,java.lang.Integer> _executionLSIDtoIdMap

MAX_PORT_EVENT_DATA_LENGTH

public static final int MAX_PORT_EVENT_DATA_LENGTH

The maximum length of the data stored in the port_event table. Larger data is stored in the data table.

See Also:

Constant Field Values

Constructor Detail

SQLRecordingV8

public SQLRecordingV8()
               throws RecordingException

Throws:

RecordingException

Method Detail

addFileForLastExecution

public void addFileForLastExecution(java.util.Map<java.lang.String,java.lang.String> metadataMap,
                                    java.io.File file)
                             throws RecordingException

Associate the contents of a file with the most recent workflow execution.

Overrides:

addFileForLastExecution in class Recording

Throws:

RecordingException

addFileForExecution

public void addFileForExecution(java.util.Map<java.lang.String,java.lang.String> metadataMap,
                                java.io.File file,
                                int execId)
                         throws RecordingException

Associate the contents of a file with the most recent workflow execution. If execId == RegEntity.UNKNOWN_ID, use last execution.

Throws:

RecordingException

attributeChanged

public void attributeChanged(Attribute attribute)
                      throws IllegalActionException

React to a change in an attribute.

Overrides:

attributeChanged in class SQLRecording

Throws:

IllegalActionException

generateParameters

public RecordingParameters generateParameters(NamedObj no)
                                       throws IllegalActionException,
                                              NameDuplicationException

Add Parameters for ProvenanceRecorder.

Overrides:

generateParameters in class SQLRecording

Throws:

IllegalActionException

NameDuplicationException

regPort

public boolean regPort(TypedIOPort port)
                throws RecordingException

Register a port or portparameter.

Overrides:

regPort in class SQLRecording

Returns:

if true, register contents of port.

Throws:

RecordingException

executionStart

public void executionStart(KeplerLSID executionLSID,
                           java.util.Date timestamp)
                    throws RecordingException

Record the starting of workflow execution.

Overrides:

executionStart in class Recording

Throws:

RecordingException

executionError

public void executionError(Nameable source,
                           java.lang.Throwable throwable,
                           KeplerLSID executionLSID)
                    throws RecordingException

An actor threw an exception.

Overrides:

executionError in class Recording

Throws:

RecordingException

executionStop

public void executionStop(KeplerLSID executionLSID,
                          java.util.Date timestamp)
                   throws RecordingException

Record the stopping of workflow execution.

Overrides:

executionStop in class Recording

Throws:

RecordingException

regContents

public boolean regContents()
                    throws RecordingException

Returns true if workflow contents should be registered.

Overrides:

regContents in class Recording

Throws:

RecordingException

regLink

public boolean regLink(NamedObj endPoint1,
                       NamedObj endPoint2)
                throws RecordingException

Register a link between two endpoints.

Overrides:

regLink in class SQLRecording

Parameters:

endPoint1 - first endpoint.

endPoint2 - second endpoint.

Returns:

if true, register contents of link.

Throws:

RecordingException

regParameter

public boolean regParameter(NamedObj parameter)
                     throws RecordingException

Register a parameter. A parameter can be any entity stored in the MoML that does not have its own regNNN() method. This can be user-level parameters (e.g., Parameter, StringParameter, etc.) or internal to Kepler (e.g., _location, semanticType000, etc.). (A "parameter" corresponds to a property in the MoML).

Overrides:

regParameter in class SQLRecordingV7

Returns:

if true, register contents of parameter.

Throws:

RecordingException

regRelation

public boolean regRelation(IORelation relation)
                    throws RecordingException

Register a relation.

Overrides:

regRelation in class SQLRecording

Returns:

if true, register contents of relation.

Throws:

RecordingException

refillPortEvent

public void refillPortEvent(IOPortRefillEvent event)
                     throws RecordingException

Record a port refill event.

Overrides:

refillPortEvent in class Recording

Throws:

RecordingException

getQueryable

public Queryable getQueryable(boolean allowReconnectWF)
                       throws QueryException,
                              RecordingException

Get a Queryable connected to the Recording output.

Overrides:

getQueryable in class Recording

Parameters:

allowReconnectWF - - false if you want to force no _reconnectWF

Throws:

QueryException - may be thrown if Queryable not implemented for the Recording type.

RecordingException

renamedWorkflow

public void renamedWorkflow(NamedObj namedObj,
                            KeplerLSID oldLSID,
                            KeplerLSID newLSID,
                            java.lang.String oldName,
                            java.lang.String newName)
                     throws RecordingException

A workflow was renamed.

Overrides:

renamedWorkflow in class Recording

Parameters:

namedObj - the workflow

oldLSID - the previous LSID

newLSID - the new LSID

oldName - the previous name

newName - the new name

Throws:

RecordingException

See Also:

WorkflowRenameListener

deleteExecutions

public int deleteExecutions(java.util.List<KeplerLSID> lsidList)
                     throws RecordingException

Delete executions given a list of execution LSIDs.

Parameters:

lsidList -

Returns:

Throws:

RecordingException

deleteWorkflowsWithNoExecutions

public int deleteWorkflowsWithNoExecutions()
                                    throws RecordingException

Delete workflows from the database that have no executions.

Returns:

the number of workflows deleted.

Throws:

RecordingException

tagAdded

public void tagAdded(TagEvent event)
              throws RecordingException

A tag was added, insert it

Overrides:

tagAdded in class Recording

Throws:

RecordingException

insertWorkflowTags

public void insertWorkflowTags(int execId)

Parse workflow moml for tags, and insert them, associated with execID

Parameters:

runLsid -

insertTag

public void insertTag(java.lang.String type,
                      java.lang.String tagStr,
                      java.lang.String urnStr,
                      int execId)
               throws RecordingException

Insert a new row into the tag table.

Throws:

RecordingException

checkIfTagAlreadyInserted

public boolean checkIfTagAlreadyInserted(int execId,
                                         java.lang.String urn)

customProvEvent

public void customProvEvent(ProvenanceEvent event)
                     throws RecordingException

Record a custom provenance event.

Overrides:

customProvEvent in class Recording

Throws:

RecordingException

tagRemoved

public void tagRemoved(TagEvent event)
                throws RecordingException

A tag was removed.

Overrides:

tagRemoved in class Recording

Throws:

RecordingException

insertPreviewRun

public boolean insertPreviewRun(WorkflowRun run)
                         throws RecordingException

If run's exec LSID does not already exist in provenance, insert WorkflowRun into provenance. This is a special case for 'preview' runs, where no other associated data (workflow data, reporting files) are inserted.

Parameters:

karFile -

run -

Throws:

RecordingException

insertHuskRun

public boolean insertHuskRun(KARFile karFile,
                             WorkflowRun run)
                      throws RecordingException

If run's exec LSID does not already exist in provenance, insert WorkflowRun into provenance. This is a special case where the run may come from a KAR, potentially from a different system.

Parameters:

karFile -

run -

Throws:

RecordingException

insertAnyHuskRunReferralList

public void insertAnyHuskRunReferralList(WorkflowRun run)

_addEntity

protected org.kepler.provenance.sql.RegEntity _addEntity(int containerId,
                                                         RegEntity.EntityType type,
                                                         java.lang.String fullName,
                                                         java.lang.String displayName,
                                                         int prevId)
                                                  throws RecordingException,
                                                         java.sql.SQLException

Add a new row to the entity table.

Overrides:

_addEntity in class SQLRecordingV7

Throws:

RecordingException

java.sql.SQLException

_addWorkflow

protected void _addWorkflow()
                     throws RecordingException

Add a new row to the workflow table.

Overrides:

_addWorkflow in class SQLRecordingV7

Throws:

RecordingException

_addWorkflowChange

protected void _addWorkflowChange()
                           throws RecordingException

Create a new row in the workflow_change table.

Overrides:

_addWorkflowChange in class SQLRecordingV7

Throws:

RecordingException

_changeEntityFullName

protected java.lang.String _changeEntityFullName(java.lang.String name)

Modify a NamedObj's full name. We remove the containing composite's name, including the period.

Overrides:

_changeEntityFullName in class SQLRecording

_checkWorkflowName

protected void _checkWorkflowName()
                           throws RecordingException

Check validity of workflow name parameter.

Overrides:

_checkWorkflowName in class SQLRecording

Throws:

RecordingException

_createPreparedStatements

protected void _createPreparedStatements()
                                  throws java.sql.SQLException

Initialize the prepared statements.

Overrides:

_createPreparedStatements in class SQLRecordingV7

Throws:

java.sql.SQLException

_createSchema

protected Schema _createSchema()

Create a Schema to reflect the v8 schema.

Overrides:

_createSchema in class SQLRecordingV7

_getMaxTokenDataSize

protected int _getMaxTokenDataSize()
                            throws java.sql.SQLException

Get the maximum size of token data that can be stored in the database.

Overrides:

_getMaxTokenDataSize in class SQLRecording

Throws:

java.sql.SQLException

_getWorkflowId

protected int _getWorkflowId()
                      throws RecordingException

Get the internal workflow id.

Overrides:

_getWorkflowId in class SQLRecording

Throws:

RecordingException

_getContainerId

protected int _getContainerId(Nameable namedObj)
                       throws RecordingException

Find the container id of an entity. Always returns RegEntity.UNKNOWN_ID since the V8 schema does not use the container id.

Overrides:

_getContainerId in class SQLRecording

Throws:

RecordingException

_nullPreparedStatements

protected void _nullPreparedStatements()

Set our prepared statements to null.

Overrides:

_nullPreparedStatements in class SQLRecordingV7

_reconnectDatabase

protected void _reconnectDatabase(boolean resetDB)
                           throws RecordingException

Reconnect to the database.

Overrides:

_reconnectDatabase in class SQLRecording

Throws:

RecordingException

_reconnectWorkflow

protected void _reconnectWorkflow()
                           throws RecordingException

Re-acquire the current workflow id.

Overrides:

_reconnectWorkflow in class SQLRecording

Throws:

RecordingException

_changeWorkflowNameColumn

protected void _changeWorkflowNameColumn(java.lang.String newName)
                                  throws RecordingException

Change the workflow.name column for the current workflow.

Throws:

RecordingException

_changeWorkflowNameColumn

protected void _changeWorkflowNameColumn(java.lang.String newName,
                                         KeplerLSID lsid)
                                  throws RecordingException

Change the workflow.name column for a specific LSID.

Throws:

RecordingException

changeExecutionLSID

public boolean changeExecutionLSID(int execId,
                                   KeplerLSID newExecLSID,
                                   Queryable q)
                            throws RecordingException

Change execution LSID for an execution Id. Does not change and returns false for attempts to change to an older or current revision, or if a QueryException, or if no such execution Id.

Overrides:

changeExecutionLSID in class Recording

Parameters:

execId -

newExecLSID -

Returns:

Throws:

RecordingException

changeExecutionType

public boolean changeExecutionType(KeplerLSID executionLSID,
                                   WorkflowRun.type type)
                            throws RecordingException

Change the execution type.

Parameters:

executionLSID -

type -

Returns:

Throws:

RecordingException

_regPortReal

protected void _regPortReal(TypedIOPort port,
                            org.kepler.provenance.sql.RegEntity re)
                     throws RecordingException

Add a port to the port table.

Overrides:

_regPortReal in class SQLRecording

Throws:

RecordingException

_recordFiringEvent

protected void _recordFiringEvent(Actor actor,
                                  FiringEvent.FiringEventType type,
                                  java.util.Date timestamp)
                           throws RecordingException

Record a specific type of firing for an actor.

Overrides:

_recordFiringEvent in class SQLRecording

Throws:

RecordingException

_recordActorFireStop

protected void _recordActorFireStop(int fireId,
                                    Actor actor,
                                    java.util.Date timestamp)
                             throws java.sql.SQLException

Record the end of an actor fire and attempt to serialize the actor's state.

Throws:

java.sql.SQLException

_recordPortEvent

protected void _recordPortEvent(IOPort port,
                                int fireId,
                                int rwfireId,
                                boolean isRead,
                                int channel,
                                Token token,
                                IOPort destPort,
                                java.util.Date timestamp)
                         throws RecordingException

Record a specific type of firing for an actor.

Overrides:

_recordPortEvent in class SQLRecording

Throws:

RecordingException

_checkData

protected java.lang.String _checkData(byte[] data)
                               throws RecordingException

Adds data to the data table if not already there.

Returns:

the md5 of the data

Throws:

RecordingException

_checkData

protected java.lang.String _checkData(java.io.File file)
                               throws RecordingException

Adds data to the data table if not already there.

Returns:

the md5 of the data

Throws:

RecordingException

_checkForFileData

protected java.lang.String _checkForFileData(Token token)
                                      throws RecordingException

See if a token contains a valid filename.

Returns:

If token contains a valid filename, and its size is less than minFileIncludeKB, then returns the MD5 of the file's contents.

Throws:

RecordingException

_dbReset

protected void _dbReset()
                 throws RecordingException

Reset when we use a different db connection.

Overrides:

_dbReset in class SQLRecording

Throws:

RecordingException

_wfReset

protected void _wfReset()

Reset when we use a different workflow.

Overrides:

_wfReset in class SQLRecordingV7

_updateParameterExecTable

protected void _updateParameterExecTable()
                                  throws RecordingException

Add all the parameter ids to the parameter_exec table.

Throws:

RecordingException