Package org.galaxyproject.gxformat2.v19_09

Class GalaxyWorkflowImpl

java.lang.Object
org.galaxyproject.gxformat2.v19_09.utils.SavableImpl
org.galaxyproject.gxformat2.v19_09.GalaxyWorkflowImpl
All Implemented Interfaces:
Documented, GalaxyWorkflow, HasUUID, Identified, Labeled, Process, Savable
public class GalaxyWorkflowImpl extends SavableImpl implements GalaxyWorkflow
Auto-generated class implementation for https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow
A Galaxy workflow description. This record corresponds to the description of a workflow that should be executable on a Galaxy server that includes the contained tool definitions.

The workflows API or the user interface of Galaxy instances that are of version 19.09 or newer should be able to import a document defining this record.

## A note about `label` field.

This is the name of the workflow in the Galaxy user interface. This is the mechanism that users will primarily identify the workflow using. Legacy support - this may also be called 'name' and Galaxy will consume the workflow document fine and treat this attribute correctly - however in order to validate against this workflow definition schema the attribute should be called `label`.

  • Constructor Summary

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

  • Method Summary

    Modifier and Type
    Method
    Description
    String
    getClass_()
    Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/class
    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>
    getId()
    Getter for property https://w3id.org/cwl/cwl#Identified/id
    The unique identifier for this object.
    List<Object>
    getInputs()
    Getter for property https://w3id.org/cwl/cwl#inputs
    Defines the input parameters of the process.
    Optional<String>
    getLabel()
    Getter for property https://w3id.org/cwl/cwl#Labeled/label
    A short, human-readable label of this object.
    List<Object>
    getOutputs()
    Getter for property https://w3id.org/cwl/cwl#outputs
    Defines the parameters representing the output of the process.
    Optional<Report>
    getReport()
    Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/report
    Workflow invocation report template.
    List<Object>
    getSteps()
    Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/steps
    The individual steps that make up the workflow.
    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

    • GalaxyWorkflowImpl

      public GalaxyWorkflowImpl(Object __doc_, String __baseUri_, LoadingOptions __loadingOptions, String __docRoot_)
      Used by RootLoader to construct instances of GalaxyWorkflowImpl.
      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 GalaxyWorkflow

    • 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 GalaxyWorkflow
      Specified by:
      getLabel in interface Labeled
      Specified by:
      getLabel in interface Process

    • 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 GalaxyWorkflow
      Specified by:
      getDoc in interface Process

    • getInputs

      public List<Object> getInputs()
      Getter for property https://w3id.org/cwl/cwl#inputs
      Defines the input parameters of the process. 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 to build a user interface for constructing the input object.

      When accepting an input object, all input parameters must have a value. If an input parameter is missing from the input object, it must be assigned a value of `null` (or the value of `default` for that parameter, if provided) for the purposes of validation and evaluation of expressions. *

      Specified by:
      getInputs in interface GalaxyWorkflow
      Specified by:
      getInputs in interface Process

    • getOutputs

      public List<Object> getOutputs()
      Getter for property https://w3id.org/cwl/cwl#outputs
      Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. *
      Specified by:
      getOutputs in interface GalaxyWorkflow
      Specified by:
      getOutputs in interface Process

    • 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 GalaxyWorkflow
      Specified by:
      getUuid in interface HasUUID

    • getClass_

      public String getClass_()
      Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/class
      Specified by:
      getClass_ in interface GalaxyWorkflow

    • getSteps

      public List<Object> getSteps()
      Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/steps
      The individual steps that make up the workflow. Each step is executed when all of its input data links are fulfilled. *
      Specified by:
      getSteps in interface GalaxyWorkflow

    • getReport

      public Optional<Report> getReport()
      Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/report
      Workflow invocation report template. *
      Specified by:
      getReport in interface GalaxyWorkflow