com.dnanexus

Class ExecutableRunner<T extends DXExecution>

java.lang.Object

com.dnanexus.ExecutableRunner<T>

Type Parameters:

T - the type of the execution that will be produced

public abstract class ExecutableRunner<T extends DXExecution>
extends Object

Collects parameters for a new run of an executable. To obtain an instance, call DXExecutable.newRun().

Field Summary

Fields

Modifier and Type	Field and Description
protected DXEnvironment	env
protected String	executableId
protected static com.fasterxml.jackson.databind.ObjectMapper	MAPPER

Method Summary

Modifier and Type	Method and Description
ExecutableRunner<T>	addTags(Collection<String> tags) Adds the specified tags to the resulting execution.
ExecutableRunner<T>	delayWorkspaceDestruction() Delays the destruction of the workspace of the resulting job so it can be examined for debugging.
ExecutableRunner<T>	dependsOn(DXDataObject dataObject) Makes the resulting execution depend on the specified data object, so that the execution will not begin until the data object is closed.
ExecutableRunner<T>	dependsOn(DXExecution execution) Makes the resulting execution depend on the specified execution, so that the former will not begin until the latter has successfully completed.
ExecutableRunner<T>	inFolder(String folder) Deprecated. Use setFolder(String) instead
ExecutableRunner<T>	inProject(DXProject project) Deprecated. Use setProject(DXProject) instead
ExecutableRunner<T>	putAllProperties(Map<String,String> properties) Sets the specified properties on the execution to be created.
ExecutableRunner<T>	putProperty(String key, String value) Sets the specified property on the execution to be created.
abstract T	run() Runs the executable.
ExecutableRunner<T>	setDetails(Object details) Sets the execution details to the JSON serialized value of the specified object.
ExecutableRunner<T>	setFolder(String folder) Sets the folder in which the execution's outputs will be deposited.
ExecutableRunner<T>	setInput(Object inputObject) Sets the input hash to the JSON serialized value of the specified object.
ExecutableRunner<T>	setName(String name) Sets the name of the resulting execution.
ExecutableRunner<T>	setProject(DXProject project) Sets the project context of the resulting execution.
ExecutableRunner<T>	setRawInput(com.fasterxml.jackson.databind.JsonNode inputHash) Sets the input hash to the specified JSON node.
ExecutableRunner<T>	withDetails(Object details) Deprecated. Use setDetails(Object) instead
ExecutableRunner<T>	withInput(Object inputObject) Deprecated. Use setInput(Object) instead
ExecutableRunner<T>	withName(String name) Deprecated. Use setName(String) instead
ExecutableRunner<T>	withRawInput(com.fasterxml.jackson.databind.JsonNode inputHash) Deprecated. Use setRawInput(JsonNode) instead

Methods inherited from class java.lang.Object

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

Field Detail

executableId

protected final String executableId

env

protected final DXEnvironment env

MAPPER

protected static final com.fasterxml.jackson.databind.ObjectMapper MAPPER

Method Detail

addTags

public ExecutableRunner<T> addTags(Collection<String> tags)

Adds the specified tags to the resulting execution.

Parameters:

tags - tags to add

Returns:

the same runner object

delayWorkspaceDestruction

public ExecutableRunner<T> delayWorkspaceDestruction()

Delays the destruction of the workspace of the resulting job so it can be examined for debugging.

Returns:

the same runner object

dependsOn

public ExecutableRunner<T> dependsOn(DXDataObject dataObject)

Makes the resulting execution depend on the specified data object, so that the execution will not begin until the data object is closed.

Parameters:

dataObject - data object to depend on

Returns:

the same runner object

dependsOn

public ExecutableRunner<T> dependsOn(DXExecution execution)

Makes the resulting execution depend on the specified execution, so that the former will not begin until the latter has successfully completed.

Parameters:

execution - execution to depend on

Returns:

the same runner object

inFolder

@Deprecated
public ExecutableRunner<T> inFolder(String folder)

Deprecated. Use setFolder(String) instead

Sets the folder in which the execution's outputs will be deposited.

Parameters:

folder - full path to folder (a String starting with "/")

Returns:

the same runner object

inProject

@Deprecated
public ExecutableRunner<T> inProject(DXProject project)

Deprecated. Use setProject(DXProject) instead

Sets the project context of the resulting execution.

Parameters:

project - project in which the executable will be run

Returns:

the same runner object

putAllProperties

public ExecutableRunner<T> putAllProperties(Map<String,String> properties)

Sets the specified properties on the execution to be created.

Parameters:

properties - Map containing non-null keys and values which will be set as property keys and values respectively

Returns:

the same Builder object

putProperty

public ExecutableRunner<T> putProperty(String key,
                                       String value)

Sets the specified property on the execution to be created.

Parameters:

key - property key to set

value - property value to set

Returns:

the same Builder object

run

public abstract T run()

Runs the executable.

Returns:

the resulting execution object

setDetails

public ExecutableRunner<T> setDetails(Object details)

Sets the execution details to the JSON serialized value of the specified object.

Parameters:

details - user-supplied metadata

Returns:

the same runner object

setFolder

public ExecutableRunner<T> setFolder(String folder)

Sets the folder in which the execution's outputs will be deposited.

Parameters:

folder - full path to folder (a String starting with "/")

Returns:

the same runner object

setInput

public ExecutableRunner<T> setInput(Object inputObject)

Sets the input hash to the JSON serialized value of the specified object.

Parameters:

inputObject - object to be JSON serialized

Returns:

the same runner object

setName

public ExecutableRunner<T> setName(String name)

Sets the name of the resulting execution.

Parameters:

name - job name

Returns:

the same runner object

setProject

public ExecutableRunner<T> setProject(DXProject project)

Sets the project context of the resulting execution.

Parameters:

project - project in which the executable will be run

Returns:

the same runner object

setRawInput

public ExecutableRunner<T> setRawInput(com.fasterxml.jackson.databind.JsonNode inputHash)

Sets the input hash to the specified JSON node.

Parameters:

inputHash -

Returns:

the same runner object

withDetails

@Deprecated
public ExecutableRunner<T> withDetails(Object details)

Deprecated. Use setDetails(Object) instead

Sets the execution details to the JSON serialized value of the specified object.

Parameters:

details - user-supplied metadata

Returns:

the same runner object

withInput

@Deprecated
public ExecutableRunner<T> withInput(Object inputObject)

Deprecated. Use setInput(Object) instead

Sets the input hash to the JSON serialized value of the specified object.

Parameters:

inputObject - object to be JSON serialized

Returns:

the same runner object

withName

@Deprecated
public ExecutableRunner<T> withName(String name)

Deprecated. Use setName(String) instead

Sets the name of the resulting execution.

Parameters:

name - job name

Returns:

the same runner object

withRawInput

@Deprecated
public ExecutableRunner<T> withRawInput(com.fasterxml.jackson.databind.JsonNode inputHash)

Deprecated. Use setRawInput(JsonNode) instead

Sets the input hash to the specified JSON node.

Parameters:

inputHash -

Returns:

the same runner object