com.dnanexus

Class DXWorkflow

java.lang.Object

com.dnanexus.DXObject

com.dnanexus.DXDataObject

com.dnanexus.DXWorkflow

All Implemented Interfaces:

DXExecutable<DXAnalysis>

public class DXWorkflow
extends DXDataObject
implements DXExecutable<DXAnalysis>

A workflow.

Note that these Java bindings do not supply any high-level way to modify the workflow. Please use the command-line tools or see the API documentation for workflows.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	DXWorkflow.Builder Builder class for creating a new DXWorkflow object.
static class	DXWorkflow.Describe Contains metadata for a workflow.
static class	DXWorkflow.Modification<T> Represents the result of a workflow-modifying operation, along with the workflow's edit version after that operation.
static class	DXWorkflow.Stage A workflow stage.

Nested classes/interfaces inherited from class com.dnanexus.DXDataObject

DXDataObject.DescribeOptions

Field Summary

Fields inherited from class com.dnanexus.DXDataObject

cachedDescribe

Fields inherited from class com.dnanexus.DXObject

dxId, env, MAPPER

Method Summary

Modifier and Type	Method and Description
DXWorkflow.Modification<DXWorkflow.Stage>	addStage(DXApplet applet, String name, Object stageInputs, int editVersion) Adds a stage to a workflow.
DXWorkflow	close() Closes the data object.
DXWorkflow	closeAndWait() Closes the data object and waits until the close operation is complete.
DXWorkflow.Describe	describe() Returns metadata about the data object.
DXWorkflow.Describe	describe(DXDataObject.DescribeOptions options) Returns metadata about the data object, specifying which optional fields are to be returned and what project to obtain project-specific metadata from.
DXWorkflow.Describe	getCachedDescribe() Returns metadata about the data object, like DXDataObject.describe(), but without making an API call.
static DXWorkflow	getInstance(String workflowId) Returns a DXWorkflow associated with an existing workflow.
static DXWorkflow	getInstance(String workflowId, DXContainer project) Returns a DXWorkflow associated with an existing workflow in a particular project or container.
static DXWorkflow	getInstanceWithEnvironment(String workflowId, DXContainer project, DXEnvironment env) Returns a DXWorkflow associated with an existing workflow in a particular project using the specified environment.
static DXWorkflow	getInstanceWithEnvironment(String workflowId, DXEnvironment env) Returns a DXWorkflow associated with an existing workflow using the specified environment.
ExecutableRunner<DXAnalysis>	newRun() Returns an object for creating a new run of this executable.
static DXWorkflow.Builder	newWorkflow() Returns a Builder object for creating a new DXWorkflow.
static DXWorkflow.Builder	newWorkflowWithEnvironment(DXEnvironment env) Returns a Builder object for creating a new DXWorkflow using the specified environment.

Methods inherited from class com.dnanexus.DXDataObject

addTags, addTypes, checkCachedDescribeAvailable, checkDXLinkFormat, equals, getLinkAsJson, getProject, hashCode, listProjects, putAllProperties, putAllProperties, putProperty, removeProperty, removeTags, removeTypes, rename, setDetails, setVisibility

Methods inherited from class com.dnanexus.DXObject

apiCallOnObject, apiCallOnObject, getId, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.dnanexus.DXExecutable

getId

Method Detail

getInstance

public static DXWorkflow getInstance(String workflowId)

Returns a DXWorkflow associated with an existing workflow.

Throws:

NullPointerException - If workflowId is null

getInstance

public static DXWorkflow getInstance(String workflowId,
                                     DXContainer project)

Returns a DXWorkflow associated with an existing workflow in a particular project or container.

Throws:

NullPointerException - If workflowId or container is null

getInstanceWithEnvironment

public static DXWorkflow getInstanceWithEnvironment(String workflowId,
                                                    DXContainer project,
                                                    DXEnvironment env)

Returns a DXWorkflow associated with an existing workflow in a particular project using the specified environment.

Throws:

NullPointerException - If workflowId or container is null

getInstanceWithEnvironment

public static DXWorkflow getInstanceWithEnvironment(String workflowId,
                                                    DXEnvironment env)

Returns a DXWorkflow associated with an existing workflow using the specified environment.

Throws:

NullPointerException - If workflowId is null

newWorkflow

public static DXWorkflow.Builder newWorkflow()

Returns a Builder object for creating a new DXWorkflow.

Returns:

a newly initialized builder object

newWorkflowWithEnvironment

public static DXWorkflow.Builder newWorkflowWithEnvironment(DXEnvironment env)

Returns a Builder object for creating a new DXWorkflow using the specified environment.

Parameters:

env - environment to use to make API calls

Returns:

a newly initialized builder object

close

public DXWorkflow close()

Description copied from class: DXDataObject

Closes the data object.

Returns the same object so you can chain calls.

Overrides:

close in class DXDataObject

Returns:

the same DXDataObject

closeAndWait

public DXWorkflow closeAndWait()

Description copied from class: DXDataObject

Closes the data object and waits until the close operation is complete.

Returns the same object so you can chain calls.

Overrides:

closeAndWait in class DXDataObject

Returns:

the same DXDataObject

describe

public DXWorkflow.Describe describe()

Description copied from class: DXDataObject

Returns metadata about the data object.

The properties and details fields will not be returned, and any project-specific metadata fields will be selected from an arbitrary project in which the requesting user has access to this object. To change either of these aspects of this behavior, use DXDataObject.describe(DescribeOptions) instead.

Overrides:

describe in class DXDataObject

Returns:

a Describe containing the data object's metadata.

describe

public DXWorkflow.Describe describe(DXDataObject.DescribeOptions options)

Description copied from class: DXDataObject

Returns metadata about the data object, specifying which optional fields are to be returned and what project to obtain project-specific metadata from.

Overrides:

describe in class DXDataObject

Parameters:

options - DescribeOptions object specifying how the describe request is to be made.

Returns:

a Describe containing the data object's metadata.

getCachedDescribe

public DXWorkflow.Describe getCachedDescribe()

Description copied from class: DXDataObject

Returns metadata about the data object, like DXDataObject.describe(), but without making an API call.

This cached describe info is only available if this object appears in the result of a DXSearch.findDataObjects() call that specified DXSearch.FindDataObjectsRequestBuilder.includeDescribeOutput(), and the describe info that is returned reflects the state of the object at the time that the search was performed.

Overrides:

getCachedDescribe in class DXDataObject

Returns:

a Describe containing the data object's metadata

newRun

public ExecutableRunner<DXAnalysis> newRun()

Description copied from interface: DXExecutable

Returns an object for creating a new run of this executable.

Specified by:

newRun in interface DXExecutable<DXAnalysis>

Returns:

executable runner

addStage

public DXWorkflow.Modification<DXWorkflow.Stage> addStage(DXApplet applet,
                                                          String name,
                                                          Object stageInputs,
                                                          int editVersion)

Adds a stage to a workflow.

Parameters:

applet - Applet to run

name - stage name

stageInputs - inputs to be provided to the applet

editVersion - current version of the workflow

Returns:

Modification object containing the new stage