Package ca.corefacility.bioinformatics.irida.model.workflow.analysis

Class ToolExecution

java.lang.Object

ca.corefacility.bioinformatics.irida.model.workflow.analysis.ToolExecution

All Implemented Interfaces:

IridaThing, Timestamped<java.lang.Long>

@Entity
public class ToolExecution
extends java.lang.Object
implements IridaThing

A historical record of how a tool was executed by a workflow execution manager to produce some set of outputs.

Constructor Summary

Constructors

Constructor	Description
ToolExecution(java.lang.Long id, java.util.Set<ToolExecution> previousSteps, java.lang.String toolName, java.lang.String toolVersion, java.lang.String executionManagerIdentifier, java.util.Map<java.lang.String,java.lang.String> executionTimeParameters)	Construct a new instance of ToolExecution.
ToolExecution(java.util.Set<ToolExecution> previousSteps, java.lang.String toolName, java.lang.String toolVersion, java.lang.String executionManagerIdentifier, java.util.Map<java.lang.String,java.lang.String> executionTimeParameters, java.lang.String commandLine)	Construct a new instance of ToolExecution.

Method Summary

Modifier and Type	Method	Description
boolean	equals(java.lang.Object o)
java.lang.String	getCommandLine()
java.util.Date	getCreatedDate()	Get the created date of the object
java.lang.String	getExecutionManagerIdentifier()
java.util.Map<java.lang.String,java.lang.String>	getExecutionTimeParameters()	Get the parameters for execution time of a pipeline
java.lang.Long	getId()	Get the numerical identifier for this object
java.lang.String	getLabel()	Get a human readable label for this object.
java.util.Set<ToolExecution>	getPreviousSteps()
java.lang.String	getToolName()
java.lang.String	getToolVersion()
int	hashCode()
boolean	isInputTool()	Indicates whether or not this tool is an input tool or data source.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface ca.corefacility.bioinformatics.irida.model.IridaThing

getIdentifier, setLabel

Constructor Detail

ToolExecution

public ToolExecution(java.util.Set<ToolExecution> previousSteps,
                     java.lang.String toolName,
                     java.lang.String toolVersion,
                     java.lang.String executionManagerIdentifier,
                     java.util.Map<java.lang.String,java.lang.String> executionTimeParameters,
                     java.lang.String commandLine)

Construct a new instance of ToolExecution.

Parameters:

previousSteps - the set of ToolExecution that led to the input of this ToolExecution.

toolName - the name of the tool that was executed.

toolVersion - the version of the tool that was executed.

executionManagerIdentifier - the execution manager identifier that this provenance was derived from (the history step in Galaxy).

executionTimeParameters - the parameters that were passed to the tool at execution time.

commandLine - the actual command line invocation that launched this tool.

ToolExecution

public ToolExecution(java.lang.Long id,
                     java.util.Set<ToolExecution> previousSteps,
                     java.lang.String toolName,
                     java.lang.String toolVersion,
                     java.lang.String executionManagerIdentifier,
                     java.util.Map<java.lang.String,java.lang.String> executionTimeParameters)

Construct a new instance of ToolExecution.

Parameters:

id - the id for the ToolExecution

previousSteps - the set of ToolExecution that led to the input of this ToolExecution.

toolName - the name of the tool that was executed.

toolVersion - the version of the tool that was executed.

executionManagerIdentifier - the execution manager identifier that this provenance was derived from (the history step in Galaxy).

executionTimeParameters - the parameters that were passed to the tool at execution time.

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

getPreviousSteps

public java.util.Set<ToolExecution> getPreviousSteps()

getToolName

public java.lang.String getToolName()

getToolVersion

public java.lang.String getToolVersion()

getCommandLine

public java.lang.String getCommandLine()

getExecutionManagerIdentifier

public java.lang.String getExecutionManagerIdentifier()

getExecutionTimeParameters

public java.util.Map<java.lang.String,java.lang.String> getExecutionTimeParameters()

Get the parameters for execution time of a pipeline

Returns:

The unescaped execution time parameters

getCreatedDate

public java.util.Date getCreatedDate()

Description copied from interface: Timestamped

Get the created date of the object

Specified by:

getCreatedDate in interface Timestamped<java.lang.Long>

Returns:

A Date object of the created date

getLabel

public java.lang.String getLabel()

Description copied from interface: IridaThing

Get a human readable label for this object.

Specified by:

getLabel in interface IridaThing

Returns:

a human-readable label for the object.

getId

public java.lang.Long getId()

Description copied from interface: IridaThing

Get the numerical identifier for this object

Specified by:

getId in interface IridaThing

Specified by:

getId in interface Timestamped<java.lang.Long>

Returns:

the numerical identifier for the object

isInputTool

public boolean isInputTool()

Indicates whether or not this tool is an input tool or data source.

Returns:

true if the tool execution is an input tool, false otherwise.