Package org.galaxyproject.gxformat2.v19_09

Class WorkflowStepImpl

java.lang.Object
org.galaxyproject.gxformat2.v19_09.utils.SavableImpl
org.galaxyproject.gxformat2.v19_09.WorkflowStepImpl
All Implemented Interfaces:
Documented, HasStepErrors, HasStepPosition, HasUUID, Identified, Labeled, ReferencesTool, Savable, WorkflowStep
public class WorkflowStepImpl extends SavableImpl implements WorkflowStep
Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#WorkflowStep
This represents a non-input step a Galaxy Workflow.

# A note about `state` and `tool_state` fields.

Only one or the other should be specified. These are two ways to represent the "state" of a tool at this workflow step. Both are essentially maps from parameter names to parameter values.

`tool_state` is much more low-level and expects a flat dictionary with each value a JSON dump. Nested tool structures such as conditionals and repeats should have all their values in the JSON dumped string. In general `tool_state` may be present in workflows exported from Galaxy but shouldn't be written by humans.

`state` can contained a typed map. Repeat values can be represented as YAML arrays. An alternative to representing `state` this way is defining inputs with default values.

  • Constructor Summary

    Constructors
    Constructor
    Description
    WorkflowStepImpl(Object __doc_, String __baseUri_, LoadingOptions __loadingOptions, String __docRoot_)
    Used by RootLoader to construct instances of WorkflowStepImpl.

  • Method Summary

    Modifier and Type
    Method
    Description
    Object
    getDoc()
    Getter for property https://w3id.org/cwl/salad#Documented/doc
    A documentation string for this object, or an array of strings which should be concatenated.
    Optional<String>
    getErrors()
    Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasStepErrors/errors
    During Galaxy export there may be some problem validating the tool state, tool used, etc..
    Optional<String>
    getId()
    Getter for property https://w3id.org/cwl/cwl#Identified/id
    The unique identifier for this object.
    Optional<List<Object>>
    getIn()
    Getter for property https://galaxyproject.org/gxformat2/v19_09#in
    Defines the input parameters of the workflow step.
    Optional<String>
    getLabel()
    Getter for property https://w3id.org/cwl/cwl#Labeled/label
    A short, human-readable label of this object.
    Optional<List<Object>>
    getOut()
    Getter for property https://galaxyproject.org/gxformat2/v19_09#out
    Defines the parameters representing the output of the process.
    Optional<StepPosition>
    getPosition()
    Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
    Optional<GalaxyWorkflow>
    getRun()
    Getter for property https://w3id.org/cwl/cwl#run
    Specifies a subworkflow to run.
    Optional<List<Object>>
    getRuntime_inputs()
    Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStep/runtime_inputs
    Optional<Object>
    getState()
    Getter for property https://galaxyproject.org/gxformat2/v19_09#state
    Structured tool state.
    Optional<String>
    getTool_id()
    Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_id
    The tool ID used to run this step of the workflow (e.g.
    Optional<ToolShedRepository>
    getTool_shed_repository()
    Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_shed_repository
    The Galaxy Tool Shed repository that should be installed in order to use this tool.
    Optional<Object>
    getTool_state()
    Getter for property https://galaxyproject.org/gxformat2/v19_09#tool_state
    Unstructured tool state.
    Optional<String>
    getTool_version()
    Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_version
    The tool version corresponding used to run this step of the workflow.
    Optional<WorkflowStepType>
    getType()
    Getter for property https://w3id.org/cwl/salad#type
    Workflow step module's type (defaults to 'tool').
    Optional<String>
    getUuid()
    Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasUUID/uuid
    UUID uniquely representing this element.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • WorkflowStepImpl

      public WorkflowStepImpl(Object __doc_, String __baseUri_, LoadingOptions __loadingOptions, String __docRoot_)
      Used by RootLoader to construct instances of WorkflowStepImpl.
      Parameters:
      __doc_ - Document fragment to load this record object from (presumably a Map).
      __baseUri_ - Base URI to generate child document IDs against.
      __loadingOptions - Context for loading URIs and populating objects.
      __docRoot_ - ID at this position in the document (if available) (maybe?)
      Throws:
      ValidationException - If the document fragment is not a Map or validation of fields fails.

  • Method Details

    • getId

      public Optional<String> getId()
      Getter for property https://w3id.org/cwl/cwl#Identified/id
      The unique identifier for this object. *
      Specified by:
      getId in interface WorkflowStep

    • getLabel

      public Optional<String> getLabel()
      Getter for property https://w3id.org/cwl/cwl#Labeled/label
      A short, human-readable label of this object. *
      Specified by:
      getLabel in interface Labeled
      Specified by:
      getLabel in interface WorkflowStep

    • getDoc

      public Object getDoc()
      Getter for property https://w3id.org/cwl/salad#Documented/doc
      A documentation string for this object, or an array of strings which should be concatenated. *
      Specified by:
      getDoc in interface Documented
      Specified by:
      getDoc in interface WorkflowStep

    • getPosition

      public Optional<StepPosition> getPosition()
      Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition/position
      Specified by:
      getPosition in interface HasStepPosition
      Specified by:
      getPosition in interface WorkflowStep

    • getTool_id

      public Optional<String> getTool_id()
      Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_id
      The tool ID used to run this step of the workflow (e.g. 'cat1' or 'toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0'). *
      Specified by:
      getTool_id in interface ReferencesTool
      Specified by:
      getTool_id in interface WorkflowStep

    • getTool_shed_repository

      public Optional<ToolShedRepository> getTool_shed_repository()
      Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_shed_repository
      The Galaxy Tool Shed repository that should be installed in order to use this tool. *
      Specified by:
      getTool_shed_repository in interface ReferencesTool
      Specified by:
      getTool_shed_repository in interface WorkflowStep

    • getTool_version

      public Optional<String> getTool_version()
      Getter for property https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool/tool_version
      The tool version corresponding used to run this step of the workflow. For tool shed installed tools, the ID generally uniquely specifies a version and this field is optional. *
      Specified by:
      getTool_version in interface ReferencesTool
      Specified by:
      getTool_version in interface WorkflowStep

    • getErrors

      public Optional<String> getErrors()
      Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasStepErrors/errors
      During Galaxy export there may be some problem validating the tool state, tool used, etc.. that will be indicated by this field. The Galaxy user should be warned of these problems before the workflow can be used in Galaxy.

      This field should not be used in human written Galaxy workflow files.

      A typical problem is the referenced tool is not installed, this can be fixed by installed the tool and re-saving the workflow and then re-exporting it. *

      Specified by:
      getErrors in interface HasStepErrors
      Specified by:
      getErrors in interface WorkflowStep

    • getUuid

      public Optional<String> getUuid()
      Getter for property https://galaxyproject.org/gxformat2/gxformat2common#HasUUID/uuid
      UUID uniquely representing this element. *
      Specified by:
      getUuid in interface HasUUID
      Specified by:
      getUuid in interface WorkflowStep

    • getIn

      public Optional<List<Object>> getIn()
      Getter for property https://galaxyproject.org/gxformat2/v19_09#in
      Defines the input parameters of the workflow step. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used build a user interface for constructing the input object. *
      Specified by:
      getIn in interface WorkflowStep

    • getOut

      public Optional<List<Object>> getOut()
      Getter for property https://galaxyproject.org/gxformat2/v19_09#out
      Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.

      This can also be called 'outputs' for legacy reasons - but the resulting workflow document is not a valid instance of this schema. *

      Specified by:
      getOut in interface WorkflowStep

    • getState

      public Optional<Object> getState()
      Getter for property https://galaxyproject.org/gxformat2/v19_09#state
      Structured tool state. *
      Specified by:
      getState in interface WorkflowStep

    • getTool_state

      public Optional<Object> getTool_state()
      Getter for property https://galaxyproject.org/gxformat2/v19_09#tool_state
      Unstructured tool state. *
      Specified by:
      getTool_state in interface WorkflowStep

    • getType

      public Optional<WorkflowStepType> getType()
      Getter for property https://w3id.org/cwl/salad#type
      Workflow step module's type (defaults to 'tool'). *
      Specified by:
      getType in interface WorkflowStep

    • getRun

      public Optional<GalaxyWorkflow> getRun()
      Getter for property https://w3id.org/cwl/cwl#run
      Specifies a subworkflow to run. *
      Specified by:
      getRun in interface WorkflowStep

    • getRuntime_inputs

      public Optional<List<Object>> getRuntime_inputs()
      Getter for property https://galaxyproject.org/gxformat2/v19_09#WorkflowStep/runtime_inputs
      Specified by:
      getRuntime_inputs in interface WorkflowStep