Package com.atgenomix.seqslab.piper.plugin.api

Class OperatorContext

java.lang.Object

com.atgenomix.seqslab.piper.plugin.api.OperatorContext

All Implemented Interfaces:

Serializable

public abstract class OperatorContext
extends Object
implements Serializable

An object used in pipeline operations to represent a persistent set of properties, inputs, and outputs. An operator context object contains a list of properties in the form of NamedValue objects. These properties represent information about the operator configuration, the environment, or the states of pipeline operations. An operator context object is created first from the task pipeline configuration of an input or output data file and then calling each operator in the pipeline execution on the default and updated context. The property keys might be fully qualified by prefixing the operator name, ex: name:key.

See Also:

• Operator
• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
Map<String,PiperValue>	inputs	An immutable map that contains NamedValue task input variables and files.
Map<String,PiperValue>	outputs	An immutable map that contains NamedValue task output variables and files.
protected Map<String,Object>	properties	A property map that contains NamedValue objects including those specific to the operator and other properties set by upstream pipeline operators.

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	OperatorContext(Map<String,Object> properties)	Creates an operator context with the specified defaults.
protected	OperatorContext(Map<String,Object> properties, Map<String,PiperValue> inputs)	Creates an operator context with the specified defaults and task inputs.
protected	OperatorContext(Map<String,Object> properties, Map<String,PiperValue> inputs, Map<String,PiperValue> outputs)	Creates an operator context with the specified defaults and task inputs and outputs.

Method Summary

Modifier and Type	Method	Description
Object	get(String key)	Get the property value
Map<String,Object>	getProperties()	Get the properties
void	setProperties(Map<String,Object> properties)	Set new properties

Methods inherited from class java.lang.Object

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

Field Details

properties

protected Map<String,Object> properties

A property map that contains NamedValue objects including those specific to the operator and other properties set by upstream pipeline operators. The keys might be fully qualified by prefixing the operator name, ex: name:key.

inputs

public Map<String,PiperValue> inputs

An immutable map that contains NamedValue task input variables and files.

outputs

public Map<String,PiperValue> outputs

An immutable map that contains NamedValue task output variables and files.

Constructor Details

OperatorContext

protected OperatorContext(Map<String,Object> properties)

Creates an operator context with the specified defaults.

Parameters:

properties - default properties

OperatorContext

protected OperatorContext(Map<String,Object> properties,
 Map<String,PiperValue> inputs)

Creates an operator context with the specified defaults and task inputs.

Parameters:

properties - default properties

inputs - task input variables and files

OperatorContext

protected OperatorContext(Map<String,Object> properties,
 Map<String,PiperValue> inputs,
 Map<String,PiperValue> outputs)

Creates an operator context with the specified defaults and task inputs and outputs.

Parameters:

properties - default properties

inputs - task input variables and files

outputs - task output variables and files

Method Details

get

public Object get(String key)

Get the property value

Parameters:

key - the property key

Returns:

the property object. return null if the key is not found.

getProperties

public Map<String,Object> getProperties()

Get the properties

Returns:

the property map

setProperties

public void setProperties(Map<String,Object> properties)

Set new properties