org.kepler.provenance

Class DefaultQuery

java.lang.Object

org.kepler.provenance.DefaultQuery

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, Queryable

Direct Known Subclasses:

ProvQuery, SQLQueryV8

public abstract class DefaultQuery
extends java.lang.Object
implements Queryable

A default implementation of Queryable. Most methods do nothing and return null.

Author:

Daniel Crawl

Constructor Summary

Constructors

Constructor and Description
DefaultQuery()

Method Summary

Modifier and Type	Method and Description
protected java.lang.Integer	_getLastExecutionId(KeplerLSID workflow) Get the last execution id for a workflow.
protected abstract boolean	_stringTokenValuesHaveSurroundingQuotes() Returns true if getTokenValue() for StringTokens has surrounding double-quotes. i.e., the value was saved using StringToken.toString() (which adds double-quotes) instead of StringToken.stringValue().
void	close()
void	disconnect() Disconnect from provenance store.
java.util.List<java.lang.Integer>	getActorFiringForToken(int tokenId, boolean read) Get the firing id(s) of the actor(s) that read or wrote a token.
java.util.List<java.lang.Integer>	getActorFiringIds(java.lang.String actorName, java.lang.Integer wfExecId) Get actor fire ids based on its full name and workflow exec ID.
java.util.List<java.lang.Integer>	getActorFirings(int wfExecId) Get all actor fire ids for a workflow exec ID.
java.lang.String	getActorName(int fireId) Get an actor's name for a firing id.
java.lang.String	getActorType(int fireId) Get an actor's type for a firing id.
java.util.List<byte[]>	getAssociatedDataForExecution(int execId, java.util.Map<java.lang.String,java.lang.String> metadataMap, boolean matchAny) Get a file associated with an execution.
java.util.Map<java.lang.String,java.lang.String>	getAssociatedKeysValuesForExecution(int execId) Get any associated keys-values for an execution.
java.lang.Integer	getChannelForToken(int tokenId, boolean read, java.lang.Integer fireId) Get the channel that a token was read or written on.
java.lang.Integer	getEntityId(java.lang.String entityName, KeplerLSID lsid) Get the id of entity.
java.lang.Integer	getEntityId(java.lang.String entityName, java.lang.String workflowName) Get the id of entity.
java.lang.String	getEntityType(java.lang.Integer entityId) Get the type of entity.
java.lang.Integer	getEntityWorkflowId(java.lang.Integer entityId) Get the workflow id of entity.
java.lang.String	getErrorForExecution(KeplerLSID lsid) Get the error for an execution.
java.lang.Integer	getExecutionForExecutionLSID(KeplerLSID runLSID) Get the execution for a specific run LSID.
java.lang.Integer	getExecutionForExecutionLSIDWithoutRevision(java.lang.String execLSIDWithoutRevision) Get execution id for an execution LSID without revision.
java.lang.Integer	getExecutionForOldestReferralExecutionLSIDWithoutRevision(java.lang.String stringWithoutRevision) Get execution id for execution that has the given LSID as its oldest referral.
java.util.List<java.lang.Integer>	getExecutionIdsForTags(java.lang.String tagsSearchString) Get execution ids for %tagsSearchString% (case insensitive)
KeplerLSID	getExecutionLSIDForExecution(java.lang.Integer execId) Get the execution LSID for a specific execution id.
java.util.List<KeplerLSID>	getExecutionLSIDs() Get a list of all execution LSIDs.
java.util.List<KeplerLSID>	getExecutionLSIDsForWorkflowRuns(java.lang.String workflowName, java.lang.String userName, java.util.Date after, java.util.Date before, int execIdAfter, int execIdBefore)
java.util.List<java.lang.Integer>	getExecutions() Get a list of all executions.
java.util.List<java.lang.Integer>	getExecutionsForAnnotation(java.lang.String annotation) Get a list of executions for a specific execution annotation.
java.util.List<java.lang.Integer>	getExecutionsForTimespan(java.util.Date start, java.util.Date end) Get executions within a timespan.
java.util.List<KeplerLSID>	getExecutionsForType(WorkflowRun.type type) Get a list of executions corresponding to a specific type.
java.util.List<java.lang.Integer>	getExecutionsForWorkflow(java.lang.String workflow) Get a list of executions for a specific workflow.
java.util.List<java.lang.Integer>	getExecutionsForWorkflowRuns(java.lang.String workflowName, java.lang.String userName) Get executions that have %workflowName% and %userName%.
java.util.List<java.lang.Integer>	getExecutionsForWorkflowRuns(java.lang.String workflowName, java.lang.String userName, java.util.Date after, java.util.Date before, int execIdAfter, int execIdBefore) Get executions that have %workflowName% and %userName%. and startTime >= after and startTime <= before.
java.util.List<java.lang.Integer>	getExecutionsForWorkflowRunsAfter(java.lang.String workflowName, java.lang.String userName, java.util.Date after) Get executions that have %workflowName% and %userName%. and startTime > after.
java.util.List<java.lang.Integer>	getExecutionsForWorkflowRunsBefore(java.lang.String workflowName, java.lang.String userName, java.util.Date before) Get exections that have %workflowName% and %userName%, and startTime < before.
java.util.Map<java.lang.String,java.lang.Long>	getExecutionTimesForActor(KeplerLSID workflow, KeplerLSID execLSID, java.lang.String actor) Get the execution times for an actor.
java.lang.String	getHostIdForExecution(java.lang.Integer execId) Get the host id for a specific execution id.
java.util.List<java.lang.Integer>	getImmediateDependencies(int tokenId) Get the token(s) that generated a token.
java.lang.String	getInputRoleForTokenAndFireId(int tokenId, int fireId) Get the input role (port name) of a token.
java.util.Map<java.lang.Integer,java.lang.Integer>	getIOBytesForPort(KeplerLSID workflow, java.lang.Integer execId, java.lang.String port, boolean read) Get the number of bytes read or written by a port.
java.lang.Integer	getLastExecutionForWorkflow(KeplerLSID lsid) Get the last execution for a workflow.
java.lang.Integer	getLastExecutionForWorkflow(java.lang.String workflow) Get the last execution for a workflow.
KeplerLSID	getLastExecutionLSIDForWorkflow(KeplerLSID lsid) Get the last execution LSID for a workflow.
KeplerLSID	getLastExecutionLSIDForWorkflow(java.lang.String workflow) Get the last execution LSID for a workflow.
java.lang.String	getMoMLForExecution(int execId) Get workflow MoML for an execution.
java.lang.String	getMoMLForExecution(KeplerLSID lsid) Get workflow MoML for an execution LSID
java.util.List<java.lang.String>	getMoMLForExecutionLSIDs(java.util.List<KeplerLSID> lsids) Get workflow MoMLs for a list of execution lsids.
java.lang.String	getOutputRoleToken(int tokenId) Get the output role (port name) of a token.
java.util.Map<java.lang.String,java.lang.String>	getParameterAndPortParameterNameValuesForFiring(int fireId) Get an actor's parameter and port parameter name value pairs for a firing id.
java.util.Map<java.lang.String,java.lang.String>	getParameterNameValuesForExecution(int execId) Get the parameter name value pairs for an execution.
java.util.Map<java.lang.String,java.lang.String>	getParameterNameValuesForFiring(int fireId) Get an actor's parameter name value pairs for a firing id.
java.util.Map<java.lang.String,java.lang.String>	getParameterNameValuesOfSpecificTypeForExecution(int execId) Get the parameter name value pairs for an execution, whose parameter type is either '.Parameter' or '.StringParameter'
java.lang.String	getParameterValueAtTime(java.util.Date timestamp, java.lang.String parameter, KeplerLSID lsid) Get the value of a parameter at a specific time.
java.lang.String	getParameterValueLatest(java.lang.String parameter, KeplerLSID lsid) Get the latest value of a parameter.
java.util.List<java.lang.String>	getPortsForActor(KeplerLSID workflow, java.lang.String actor) Get the ports for an actor.
java.util.Map<NamedOntClass,java.lang.String>	getTagClassesForExecutionId(int execId) Get a map of tags and their types (context, or tagee, currently "run" or "workflow") for an executionLSID
java.util.List<java.lang.String>	getTagsForExecutionId(int execId) Get tags for an execution LSID
java.util.Date	getTimestampForTokenWrite(java.lang.Integer tokenId) Get the timestamp when a token was written.
java.util.Date[]	getTimestampsForActorFiring(int fireId) Get the start and end timestamps of an actor firing.
java.util.Date[]	getTimestampsForExecution(int execId) Get the start and end timestamps of an execution.
java.util.Date[]	getTimestampsForTokenRead(java.lang.Integer tokenId) Get the timestamp(s) when a token was read.
Token	getToken(int tokenId) Get the Token.
java.util.List<java.lang.Integer>	getTokensForExecution(int execId, boolean last) Get an sequence of tokens for an execution.
java.util.List<java.lang.Integer>	getTokensForExecution(int execId, java.lang.Integer portId, boolean last) Get an sequence of tokens for an execution.
java.util.List<java.lang.Integer>	getTokensForFiring(int fireId, boolean read) Get tokens for a firing.
java.lang.String	getTokenType(int tokenId) Get the type of a token.
java.lang.String	getTokenValue(int tokenId) Get the value of a token.
long	getTotalExecutionTimeForActor(KeplerLSID workflow, KeplerLSID execLSID, java.lang.String actor) Get the total execution time for an actor.
java.lang.Integer	getTotalIOBytesForActor(KeplerLSID workflow, java.lang.Integer execId, java.lang.String actor, boolean read) Get the total number of bytes read or or written by an actor over all its ports.
java.lang.String	getTypeForTag(java.lang.String conceptId) Get the type of a tag, null if none
java.lang.String	getUserForExecution(java.lang.Integer execId) Get the user for a specific execution id.
java.lang.String	getUserForExecution(KeplerLSID execLSID) Get the user for a specific execution LSID.
NamedObj	getWorkflowForExecution(java.lang.Integer execId) Get the workflow object for a execution id.
java.lang.String	getWorkflowName(KeplerLSID lsid) Get a workflow name.
java.lang.String	getWorkflowNameForExecution(KeplerLSID lsid) Get a workflow name for an execution LSID.
java.util.Map<KeplerLSID,WorkflowRun>	getWorkflowRunsForExecutionLSIDs(java.util.List<KeplerLSID> executions) Get "workflow runs" for a list of execution LSIDs.
java.util.List<WorkflowRun>	getWorkflowRunsForUser(java.lang.String user) Get workflow runs for a user.
java.util.List<java.lang.String>	getWorkflows() Get a list of workflow names.
boolean	isErrorForExecution(KeplerLSID executionLSID) Returns true if the execution had an error.
boolean	isImportedExecution(KeplerLSID executionLSID) See if an execution appears to be imported.

Methods inherited from class java.lang.Object

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

Constructor Detail

DefaultQuery

public DefaultQuery()

Method Detail

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Throws:

java.io.IOException

disconnect

public void disconnect()
                throws QueryException

Description copied from interface: Queryable

Disconnect from provenance store.

Specified by:

disconnect in interface Queryable

Throws:

QueryException

getWorkflows

public java.util.List<java.lang.String> getWorkflows()
                                              throws QueryException

Description copied from interface: Queryable

Get a list of workflow names.

Specified by:

getWorkflows in interface Queryable

Throws:

QueryException

getWorkflowName

public java.lang.String getWorkflowName(KeplerLSID lsid)
                                 throws QueryException

Description copied from interface: Queryable

Get a workflow name.

Specified by:

getWorkflowName in interface Queryable

Parameters:

lsid - the workflow's LSID.

Returns:

the workflow name if found, otherwise null.

Throws:

QueryException

getWorkflowNameForExecution

public java.lang.String getWorkflowNameForExecution(KeplerLSID lsid)
                                             throws QueryException

Description copied from interface: Queryable

Get a workflow name for an execution LSID.

Specified by:

getWorkflowNameForExecution in interface Queryable

Parameters:

lsid - the execution LSID.

Returns:

the workflow name if found, otherwise null.

Throws:

QueryException

getExecutions

public java.util.List<java.lang.Integer> getExecutions()
                                                throws QueryException

Description copied from interface: Queryable

Get a list of all executions.

Specified by:

getExecutions in interface Queryable

Throws:

QueryException

getExecutionLSIDs

public java.util.List<KeplerLSID> getExecutionLSIDs()
                                             throws QueryException

Description copied from interface: Queryable

Get a list of all execution LSIDs.

Specified by:

getExecutionLSIDs in interface Queryable

Throws:

QueryException

getExecutionsForWorkflow

public java.util.List<java.lang.Integer> getExecutionsForWorkflow(java.lang.String workflow)
                                                           throws QueryException

Description copied from interface: Queryable

Get a list of executions for a specific workflow.

Specified by:

getExecutionsForWorkflow in interface Queryable

Throws:

QueryException

getExecutionForExecutionLSID

public java.lang.Integer getExecutionForExecutionLSID(KeplerLSID runLSID)
                                               throws QueryException

Description copied from interface: Queryable

Get the execution for a specific run LSID. If no execution exists, returns null.

Specified by:

getExecutionForExecutionLSID in interface Queryable

Throws:

QueryException

getExecutionLSIDForExecution

public KeplerLSID getExecutionLSIDForExecution(java.lang.Integer execId)
                                        throws QueryException

Description copied from interface: Queryable

Get the execution LSID for a specific execution id. If no execution exists, returns null.

Specified by:

getExecutionLSIDForExecution in interface Queryable

Throws:

QueryException

getExecutionsForAnnotation

public java.util.List<java.lang.Integer> getExecutionsForAnnotation(java.lang.String annotation)
                                                             throws QueryException

Description copied from interface: Queryable

Get a list of executions for a specific execution annotation.

Specified by:

getExecutionsForAnnotation in interface Queryable

Throws:

QueryException

getTimestampsForExecution

public java.util.Date[] getTimestampsForExecution(int execId)
                                           throws QueryException

Description copied from interface: Queryable

Get the start and end timestamps of an execution.

Specified by:

getTimestampsForExecution in interface Queryable

Parameters:

execId - the execution id

Returns:

a two-element array: the first entry is the start timestamp, and the second is the end timestamp. If the execution id is not found, returns null.

Throws:

QueryException

getMoMLForExecution

public java.lang.String getMoMLForExecution(int execId)
                                     throws QueryException

Description copied from interface: Queryable

Get workflow MoML for an execution.

Specified by:

getMoMLForExecution in interface Queryable

Throws:

QueryException

getMoMLForExecution

public java.lang.String getMoMLForExecution(KeplerLSID lsid)
                                     throws QueryException

Description copied from interface: Queryable

Get workflow MoML for an execution LSID

Specified by:

getMoMLForExecution in interface Queryable

Throws:

QueryException

getMoMLForExecutionLSIDs

public java.util.List<java.lang.String> getMoMLForExecutionLSIDs(java.util.List<KeplerLSID> lsids)
                                                          throws QueryException

Description copied from interface: Queryable

Get workflow MoMLs for a list of execution lsids. Only returns one copy of any duplicates.

Specified by:

getMoMLForExecutionLSIDs in interface Queryable

Throws:

QueryException

getWorkflowForExecution

public NamedObj getWorkflowForExecution(java.lang.Integer execId)
                                 throws QueryException

Get the workflow object for a execution id.

Specified by:

getWorkflowForExecution in interface Queryable

Throws:

QueryException

getExecutionsForTimespan

public java.util.List<java.lang.Integer> getExecutionsForTimespan(java.util.Date start,
                                                                  java.util.Date end)
                                                           throws QueryException

Description copied from interface: Queryable

Get executions within a timespan.

Specified by:

getExecutionsForTimespan in interface Queryable

Throws:

QueryException

getExecutionsForWorkflowRuns

public java.util.List<java.lang.Integer> getExecutionsForWorkflowRuns(java.lang.String workflowName,
                                                                      java.lang.String userName)
                                                               throws QueryException

Description copied from interface: Queryable

Get executions that have %workflowName% and %userName%.

Specified by:

getExecutionsForWorkflowRuns in interface Queryable

Throws:

QueryException

getExecutionsForWorkflowRunsAfter

public java.util.List<java.lang.Integer> getExecutionsForWorkflowRunsAfter(java.lang.String workflowName,
                                                                           java.lang.String userName,
                                                                           java.util.Date after)
                                                                    throws QueryException

Description copied from interface: Queryable

Get executions that have %workflowName% and %userName%. and startTime > after.

Specified by:

getExecutionsForWorkflowRunsAfter in interface Queryable

Throws:

QueryException

getExecutionsForWorkflowRuns

public java.util.List<java.lang.Integer> getExecutionsForWorkflowRuns(java.lang.String workflowName,
                                                                      java.lang.String userName,
                                                                      java.util.Date after,
                                                                      java.util.Date before,
                                                                      int execIdAfter,
                                                                      int execIdBefore)
                                                               throws QueryException

Description copied from interface: Queryable

Get executions that have %workflowName% and %userName%. and startTime >= after and startTime <= before.

Specified by:

getExecutionsForWorkflowRuns in interface Queryable

Throws:

QueryException

getExecutionLSIDsForWorkflowRuns

public java.util.List<KeplerLSID> getExecutionLSIDsForWorkflowRuns(java.lang.String workflowName,
                                                                   java.lang.String userName,
                                                                   java.util.Date after,
                                                                   java.util.Date before,
                                                                   int execIdAfter,
                                                                   int execIdBefore)
                                                            throws QueryException

Specified by:

getExecutionLSIDsForWorkflowRuns in interface Queryable

Throws:

QueryException

getExecutionsForWorkflowRunsBefore

public java.util.List<java.lang.Integer> getExecutionsForWorkflowRunsBefore(java.lang.String workflowName,
                                                                            java.lang.String userName,
                                                                            java.util.Date before)
                                                                     throws QueryException

Description copied from interface: Queryable

Get exections that have %workflowName% and %userName%, and startTime < before.

Specified by:

getExecutionsForWorkflowRunsBefore in interface Queryable

Throws:

QueryException

getLastExecutionForWorkflow

public java.lang.Integer getLastExecutionForWorkflow(KeplerLSID lsid)
                                              throws QueryException

Description copied from interface: Queryable

Get the last execution for a workflow. NOTE: the LSID revision is ignored.

Specified by:

getLastExecutionForWorkflow in interface Queryable

Parameters:

lsid - the workflow lsid.

Returns:

if workflow has been executed, the last execution id. otherwise, returns null.

Throws:

QueryException

getLastExecutionForWorkflow

public java.lang.Integer getLastExecutionForWorkflow(java.lang.String workflow)
                                              throws QueryException

Description copied from interface: Queryable

Get the last execution for a workflow.

Specified by:

getLastExecutionForWorkflow in interface Queryable

Parameters:

workflow - the workflow name

Returns:

if workflow has been executed, the last execution id. otherwise, returns null.

Throws:

QueryException

getLastExecutionLSIDForWorkflow

public KeplerLSID getLastExecutionLSIDForWorkflow(java.lang.String workflow)
                                           throws QueryException

Description copied from interface: Queryable

Get the last execution LSID for a workflow.

Specified by:

getLastExecutionLSIDForWorkflow in interface Queryable

Parameters:

workflow - the workflow name.

Returns:

execution lsid

Throws:

QueryException

getLastExecutionLSIDForWorkflow

public KeplerLSID getLastExecutionLSIDForWorkflow(KeplerLSID lsid)
                                           throws QueryException

Description copied from interface: Queryable

Get the last execution LSID for a workflow.

Specified by:

getLastExecutionLSIDForWorkflow in interface Queryable

Parameters:

lsid - the workflow LSID.

Returns:

execution lsid

Throws:

QueryException

getErrorForExecution

public java.lang.String getErrorForExecution(KeplerLSID lsid)
                                      throws QueryException

Description copied from interface: Queryable

Get the error for an execution. Returns null if no error message was found. NOTE: returning null is not an indication if the execution had an error.

Specified by:

getErrorForExecution in interface Queryable

Parameters:

lsid - the workflow execution lsid.

Throws:

QueryException

See Also:

isErrorForExecution

isErrorForExecution

public boolean isErrorForExecution(KeplerLSID executionLSID)
                            throws QueryException

Description copied from interface: Queryable

Returns true if the execution had an error.

Specified by:

isErrorForExecution in interface Queryable

Throws:

QueryException

getTokensForExecution

public java.util.List<java.lang.Integer> getTokensForExecution(int execId,
                                                               boolean last)
                                                        throws QueryException

Get an sequence of tokens for an execution.

Specified by:

getTokensForExecution in interface Queryable

Parameters:

execId - the execution id

last - if true, the sequence starts at the last token created and goes backwards to the first; otherwise the sequence starts at the first.

Throws:

QueryException

getTokensForExecution

public java.util.List<java.lang.Integer> getTokensForExecution(int execId,
                                                               java.lang.Integer portId,
                                                               boolean last)
                                                        throws QueryException

Get an sequence of tokens for an execution.

Specified by:

getTokensForExecution in interface Queryable

Parameters:

execId - the execution id

portId - the port id. If null, returns the ids of tokens read in entire execution.

last - if true, the sequence starts at the last token created and goes backwards to the first; otherwise the sequence starts at the first.

Throws:

QueryException

getActorFiringForToken

public java.util.List<java.lang.Integer> getActorFiringForToken(int tokenId,
                                                                boolean read)
                                                         throws QueryException

Get the firing id(s) of the actor(s) that read or wrote a token.

Specified by:

getActorFiringForToken in interface Queryable

Parameters:

tokenId - the token id

read - If true, return the actor(s) firing id(s) that read the token. Otherwise, return the actor firing that wrote the token.

Throws:

QueryException

getTokensForFiring

public java.util.List<java.lang.Integer> getTokensForFiring(int fireId,
                                                            boolean read)
                                                     throws QueryException

Description copied from interface: Queryable

Get tokens for a firing.

Specified by:

getTokensForFiring in interface Queryable

Parameters:

fireId - the firing id

read - if true, get the tokens read; otherwise get the tokens written.

Throws:

QueryException

getToken

public Token getToken(int tokenId)
               throws QueryException

Get the Token.

Specified by:

getToken in interface Queryable

Throws:

QueryException

getTokenValue

public java.lang.String getTokenValue(int tokenId)
                               throws QueryException

Description copied from interface: Queryable

Get the value of a token.

Specified by:

getTokenValue in interface Queryable

Throws:

QueryException

getTokenType

public java.lang.String getTokenType(int tokenId)
                              throws QueryException

Description copied from interface: Queryable

Get the type of a token.

Specified by:

getTokenType in interface Queryable

Throws:

QueryException

getChannelForToken

public java.lang.Integer getChannelForToken(int tokenId,
                                            boolean read,
                                            java.lang.Integer fireId)
                                     throws QueryException

Get the channel that a token was read or written on.

Specified by:

getChannelForToken in interface Queryable

Parameters:

tokenId - the token id

read - if true, return the channel the token was read on. otherwise, return the channel the token was written on.

fireId - the actor firing id. can be null for writes, but must be specified for reads.

Returns:

the channel the token was read or written on.

Throws:

QueryException

getActorName

public java.lang.String getActorName(int fireId)
                              throws QueryException

Description copied from interface: Queryable

Get an actor's name for a firing id.

Specified by:

getActorName in interface Queryable

Throws:

QueryException

getActorType

public java.lang.String getActorType(int fireId)
                              throws QueryException

Description copied from interface: Queryable

Get an actor's type for a firing id.

Specified by:

getActorType in interface Queryable

Throws:

QueryException

getEntityId

public java.lang.Integer getEntityId(java.lang.String entityName,
                                     KeplerLSID lsid)
                              throws QueryException

Description copied from interface: Queryable

Get the id of entity. If entity is not found, returns null.

Specified by:

getEntityId in interface Queryable

Parameters:

entityName - name of entity.

lsid - the workflow LSID. NOTE: the revision is ignored.

Throws:

QueryException

getEntityId

public java.lang.Integer getEntityId(java.lang.String entityName,
                                     java.lang.String workflowName)
                              throws QueryException

Description copied from interface: Queryable

Get the id of entity. If workflow or entity is not found, returns null.

Specified by:

getEntityId in interface Queryable

Parameters:

entityName - the name of the entity.

workflowName - the name of the workflow.

Throws:

QueryException

getEntityType

public java.lang.String getEntityType(java.lang.Integer entityId)
                               throws QueryException

Description copied from interface: Queryable

Get the type of entity.

Specified by:

getEntityType in interface Queryable

Throws:

QueryException

getEntityWorkflowId

public java.lang.Integer getEntityWorkflowId(java.lang.Integer entityId)
                                      throws QueryException

Description copied from interface: Queryable

Get the workflow id of entity.

Specified by:

getEntityWorkflowId in interface Queryable

Throws:

QueryException

getParameterNameValuesForFiring

public java.util.Map<java.lang.String,java.lang.String> getParameterNameValuesForFiring(int fireId)
                                                                                 throws QueryException

Description copied from interface: Queryable

Get an actor's parameter name value pairs for a firing id. NOTE: Parameter values may change during a firing; this method returns the values at the start of the firing.

Specified by:

getParameterNameValuesForFiring in interface Queryable

Throws:

QueryException

getParameterNameValuesForExecution

public java.util.Map<java.lang.String,java.lang.String> getParameterNameValuesForExecution(int execId)
                                                                                    throws QueryException

Description copied from interface: Queryable

Get the parameter name value pairs for an execution. NOTE: Parameter values may change during an execution; this method returns the values at the start of the execution.

Specified by:

getParameterNameValuesForExecution in interface Queryable

Throws:

QueryException

getParameterValueLatest

public java.lang.String getParameterValueLatest(java.lang.String parameter,
                                                KeplerLSID lsid)
                                         throws QueryException

Description copied from interface: Queryable

Get the latest value of a parameter.

Specified by:

getParameterValueLatest in interface Queryable

Parameters:

parameter - the parameter name.

lsid - the workflow lsid

Returns:

the latest value of the parameter. If the workflow LSID or parameter name cannot be found, returns null.

Throws:

QueryException

getParameterValueAtTime

public java.lang.String getParameterValueAtTime(java.util.Date timestamp,
                                                java.lang.String parameter,
                                                KeplerLSID lsid)
                                         throws QueryException

Description copied from interface: Queryable

Get the value of a parameter at a specific time.

Specified by:

getParameterValueAtTime in interface Queryable

Parameters:

timestamp - the time

parameter - the parameter name

lsid - the workflow lsid

Returns:

the value of the parameter at the specified time. If the workflow LSID or parameter name cannot be found, returns null.

Throws:

QueryException

getImmediateDependencies

public java.util.List<java.lang.Integer> getImmediateDependencies(int tokenId)
                                                           throws QueryException

Description copied from interface: Queryable

Get the token(s) that generated a token.

Specified by:

getImmediateDependencies in interface Queryable

Throws:

QueryException

getAssociatedDataForExecution

public java.util.List<byte[]> getAssociatedDataForExecution(int execId,
                                                            java.util.Map<java.lang.String,java.lang.String> metadataMap,
                                                            boolean matchAny)
                                                     throws QueryException

Description copied from interface: Queryable

Get a file associated with an execution.

Specified by:

getAssociatedDataForExecution in interface Queryable

Throws:

QueryException

getAssociatedKeysValuesForExecution

public java.util.Map<java.lang.String,java.lang.String> getAssociatedKeysValuesForExecution(int execId)
                                                                                     throws QueryException

Get any associated keys-values for an execution.

Specified by:

getAssociatedKeysValuesForExecution in interface Queryable

Throws:

QueryException

getWorkflowRunsForExecutionLSIDs

public java.util.Map<KeplerLSID,WorkflowRun> getWorkflowRunsForExecutionLSIDs(java.util.List<KeplerLSID> executions)
                                                                       throws QueryException

Description copied from interface: Queryable

Get "workflow runs" for a list of execution LSIDs. A 'workflow run' is a group of useful information related to an execution.

Specified by:

getWorkflowRunsForExecutionLSIDs in interface Queryable

Throws:

QueryException

getWorkflowRunsForUser

public java.util.List<WorkflowRun> getWorkflowRunsForUser(java.lang.String user)
                                                   throws QueryException

Get workflow runs for a user.

Specified by:

getWorkflowRunsForUser in interface Queryable

Throws:

QueryException

getExecutionIdsForTags

public java.util.List<java.lang.Integer> getExecutionIdsForTags(java.lang.String tagsSearchString)
                                                         throws QueryException

Description copied from interface: Queryable

Get execution ids for %tagsSearchString% (case insensitive)

Specified by:

getExecutionIdsForTags in interface Queryable

Throws:

QueryException

getTagsForExecutionId

public java.util.List<java.lang.String> getTagsForExecutionId(int execId)
                                                       throws QueryException

Description copied from interface: Queryable

Get tags for an execution LSID

Specified by:

getTagsForExecutionId in interface Queryable

Throws:

QueryException

getTypeForTag

public java.lang.String getTypeForTag(java.lang.String conceptId)

Description copied from interface: Queryable

Get the type of a tag, null if none

Specified by:

getTypeForTag in interface Queryable

getTagClassesForExecutionId

public java.util.Map<NamedOntClass,java.lang.String> getTagClassesForExecutionId(int execId)
                                                                          throws QueryException

Description copied from interface: Queryable

Get a map of tags and their types (context, or tagee, currently "run" or "workflow") for an executionLSID

Specified by:

getTagClassesForExecutionId in interface Queryable

Throws:

QueryException

getExecutionForExecutionLSIDWithoutRevision

public java.lang.Integer getExecutionForExecutionLSIDWithoutRevision(java.lang.String execLSIDWithoutRevision)
                                                              throws QueryException

Description copied from interface: Queryable

Get execution id for an execution LSID without revision.

Specified by:

getExecutionForExecutionLSIDWithoutRevision in interface Queryable

Throws:

QueryException

getExecutionForOldestReferralExecutionLSIDWithoutRevision

public java.lang.Integer getExecutionForOldestReferralExecutionLSIDWithoutRevision(java.lang.String stringWithoutRevision)
                                                                            throws QueryException

Description copied from interface: Queryable

Get execution id for execution that has the given LSID as its oldest referral.

Specified by:

getExecutionForOldestReferralExecutionLSIDWithoutRevision in interface Queryable

Throws:

QueryException

getExecutionsForType

public java.util.List<KeplerLSID> getExecutionsForType(WorkflowRun.type type)
                                                throws QueryException

Description copied from interface: Queryable

Get a list of executions corresponding to a specific type.

Specified by:

getExecutionsForType in interface Queryable

Throws:

QueryException

isImportedExecution

public boolean isImportedExecution(KeplerLSID executionLSID)
                            throws QueryException

Description copied from interface: Queryable

See if an execution appears to be imported.

Specified by:

isImportedExecution in interface Queryable

Throws:

QueryException

getPortsForActor

public java.util.List<java.lang.String> getPortsForActor(KeplerLSID workflow,
                                                         java.lang.String actor)
                                                  throws QueryException

Description copied from interface: Queryable

Get the ports for an actor.

Specified by:

getPortsForActor in interface Queryable

Parameters:

workflow - the LSID of the workflow

actor - the fully-qualified name of the actor

Returns:

a list of fully-qualified names of ports of the actor

Throws:

QueryException

getUserForExecution

public java.lang.String getUserForExecution(java.lang.Integer execId)
                                     throws QueryException

Description copied from interface: Queryable

Get the user for a specific execution id.

Specified by:

getUserForExecution in interface Queryable

Throws:

QueryException

getUserForExecution

public java.lang.String getUserForExecution(KeplerLSID execLSID)
                                     throws QueryException

Description copied from interface: Queryable

Get the user for a specific execution LSID.

Specified by:

getUserForExecution in interface Queryable

Throws:

QueryException

getHostIdForExecution

public java.lang.String getHostIdForExecution(java.lang.Integer execId)
                                       throws QueryException

Description copied from interface: Queryable

Get the host id for a specific execution id.

Specified by:

getHostIdForExecution in interface Queryable

Throws:

QueryException

getOutputRoleToken

public java.lang.String getOutputRoleToken(int tokenId)
                                    throws QueryException

Description copied from interface: Queryable

Get the output role (port name) of a token.

Specified by:

getOutputRoleToken in interface Queryable

Throws:

QueryException

getInputRoleForTokenAndFireId

public java.lang.String getInputRoleForTokenAndFireId(int tokenId,
                                                      int fireId)
                                               throws QueryException

Description copied from interface: Queryable

Get the input role (port name) of a token.

Specified by:

getInputRoleForTokenAndFireId in interface Queryable

Throws:

QueryException

getParameterNameValuesOfSpecificTypeForExecution

public java.util.Map<java.lang.String,java.lang.String> getParameterNameValuesOfSpecificTypeForExecution(int execId)
                                                                                                  throws QueryException

Description copied from interface: Queryable

Get the parameter name value pairs for an execution, whose parameter type is either '.Parameter' or '.StringParameter'

Specified by:

getParameterNameValuesOfSpecificTypeForExecution in interface Queryable

Throws:

QueryException

getTimestampsForActorFiring

public java.util.Date[] getTimestampsForActorFiring(int fireId)
                                             throws QueryException

Description copied from interface: Queryable

Get the start and end timestamps of an actor firing.

Specified by:

getTimestampsForActorFiring in interface Queryable

Throws:

QueryException

getActorFiringIds

public java.util.List<java.lang.Integer> getActorFiringIds(java.lang.String actorName,
                                                           java.lang.Integer wfExecId)
                                                    throws QueryException

Description copied from interface: Queryable

Get actor fire ids based on its full name and workflow exec ID.

Specified by:

getActorFiringIds in interface Queryable

Throws:

QueryException

getParameterAndPortParameterNameValuesForFiring

public java.util.Map<java.lang.String,java.lang.String> getParameterAndPortParameterNameValuesForFiring(int fireId)
                                                                                                 throws QueryException

Description copied from interface: Queryable

Get an actor's parameter and port parameter name value pairs for a firing id. NOTE: Parameter values may change during a firing; this method returns the values at the start of the firing.

Specified by:

getParameterAndPortParameterNameValuesForFiring in interface Queryable

Throws:

QueryException

getActorFirings

public java.util.List<java.lang.Integer> getActorFirings(int wfExecId)
                                                  throws QueryException

Description copied from interface: Queryable

Get all actor fire ids for a workflow exec ID.

Specified by:

getActorFirings in interface Queryable

Throws:

QueryException

getTotalExecutionTimeForActor

public long getTotalExecutionTimeForActor(KeplerLSID workflow,
                                          KeplerLSID execLSID,
                                          java.lang.String actor)
                                   throws QueryException

Get the total execution time for an actor.

Specified by:

getTotalExecutionTimeForActor in interface Queryable

Parameters:

workflow - the workflow LSID. If null, must specify execution id.

execLSID - the execution id. If null, use the last execution of the workflow.

actor - the full actor name.

Returns:

the total time execution time of the actor, in milliseconds.

Throws:

QueryException

getExecutionTimesForActor

public java.util.Map<java.lang.String,java.lang.Long> getExecutionTimesForActor(KeplerLSID workflow,
                                                                                KeplerLSID execLSID,
                                                                                java.lang.String actor)
                                                                         throws QueryException

Get the execution times for an actor.

Specified by:

getExecutionTimesForActor in interface Queryable

Parameters:

workflow - the workflow LSID. If null, must specify execution id.

execLSID - the execution LSID. If null, the last execution of the workflow is used.

actor - the full actor name.

Returns:

a map of actor fire id to execution time pairs. if a firing does not have a valid start or stop time, the firing is not included in the result.

Throws:

QueryException

getIOBytesForPort

public java.util.Map<java.lang.Integer,java.lang.Integer> getIOBytesForPort(KeplerLSID workflow,
                                                                            java.lang.Integer execId,
                                                                            java.lang.String port,
                                                                            boolean read)
                                                                     throws QueryException

Get the number of bytes read or written by a port.

Specified by:

getIOBytesForPort in interface Queryable

Parameters:

workflow - the workflow LSID. If null, must specify execution id.

execId - the execution id. If null, the last execution of the workflow is used.

port - the full port name.

read - If true, get the bytes read. Otherwise, get the bytes written.

Returns:

a map of port event id to bytes read/written.

Throws:

QueryException

getTotalIOBytesForActor

public java.lang.Integer getTotalIOBytesForActor(KeplerLSID workflow,
                                                 java.lang.Integer execId,
                                                 java.lang.String actor,
                                                 boolean read)
                                          throws QueryException

Get the total number of bytes read or or written by an actor over all its ports.

Specified by:

getTotalIOBytesForActor in interface Queryable

Parameters:

workflow - the workflow LSID. If null, specify the execution id.

execId - the execution id. If null, the last execution of the workflow is used.

actor - the full actor name.

read - If true, get the bytes read. Otherwise, get the bytes written.

Throws:

QueryException

getTimestampsForTokenRead

public java.util.Date[] getTimestampsForTokenRead(java.lang.Integer tokenId)
                                           throws QueryException

Get the timestamp(s) when a token was read. If a token was never read, this can return null or an empty array.

Specified by:

getTimestampsForTokenRead in interface Queryable

Throws:

QueryException

getTimestampForTokenWrite

public java.util.Date getTimestampForTokenWrite(java.lang.Integer tokenId)
                                         throws QueryException

Get the timestamp when a token was written.

Specified by:

getTimestampForTokenWrite in interface Queryable

Throws:

QueryException

_getLastExecutionId

protected java.lang.Integer _getLastExecutionId(KeplerLSID workflow)
                                         throws QueryException

Get the last execution id for a workflow. If no execution id found, throws exception.

Throws:

QueryException

_stringTokenValuesHaveSurroundingQuotes

protected abstract boolean _stringTokenValuesHaveSurroundingQuotes()

Returns true if getTokenValue() for StringTokens has surrounding double-quotes. i.e., the value was saved using StringToken.toString() (which adds double-quotes) instead of StringToken.stringValue().