workflows

Documentation

Overview

workflows models represent and manipulate workflows within a Galaxy instance Relevant api endpoints are: `/api/workflows`, `/api/invocations`

Index

• Constants
• func Repositories(workflow string) ([]*repositories.Repository, error)
• type StoredWorkflow
  • func Get(ctx context.Context, g *blend4go.GalaxyInstance, id blend4go.GalaxyID) (*StoredWorkflow, error)
  • func List(ctx context.Context, g *blend4go.GalaxyInstance, ...) ([]*StoredWorkflow, error)
  • func NewStoredWorkflow(ctx context.Context, g *blend4go.GalaxyInstance, j string, ...) (*StoredWorkflow, error)
  • func (w *StoredWorkflow) Delete(ctx context.Context) error
  • func (w *StoredWorkflow) Download(ctx context.Context) (string, error)
  • func (w *StoredWorkflow) GetBasePath() string
  • func (w *StoredWorkflow) GetID() blend4go.GalaxyID
  • func (w *StoredWorkflow) Invoke(ctx context.Context) error
  • func (w *StoredWorkflow) Repositories(ctx context.Context) ([]*repositories.Repository, error)
  • func (w *StoredWorkflow) SetGalaxyInstance(g *blend4go.GalaxyInstance)
  • func (w *StoredWorkflow) SetID(id blend4go.GalaxyID)
  • func (w *StoredWorkflow) Update(ctx context.Context, j string) error
• type StoredWorkflowInput
• type StoredWorkflowInputStep
• type StoredWorkflowStep
• type WorkflowInvocation
  • func (w *WorkflowInvocation) GetBasePath() string
  • func (w *WorkflowInvocation) GetID() blend4go.GalaxyID
  • func (w *WorkflowInvocation) SetGalaxyInstance(g *blend4go.GalaxyInstance)
  • func (w *WorkflowInvocation) SetID(id blend4go.GalaxyID)
• type WorkflowInvocationStep

Constants

const BasePath = "/api/workflows"

Functions

func Repositories

func Repositories(workflow string) ([]*repositories.Repository, error)

Types

type StoredWorkflow

type StoredWorkflow struct {
	Id                 blend4go.GalaxyID               `json:"id,omitempty"`
	Name               string                          `json:"name,omitempty"`
	Tags               []string                        `json:"tags,omitempty"`
	Deleted            bool                            `json:"deleted,omitempty"`
	LatestWorkflowUuid string                          `json:"latest_workflow_uuid,omitempty"`
	ShowInToolPanel    bool                            `json:"show_in_tool_panel,omitempty"`
	Url                string                          `json:"url,omitempty"`
	NumberOfSteps      uint                            `json:"number_of_steps,omitempty"`
	Published          bool                            `json:"published,omitempty"`
	Owner              string                          `json:"owner,omitempty"`
	ModelClass         string                          `json:"model_class,omitempty"`
	Inputs             map[string]*StoredWorkflowInput `json:"inputs,omitempty"`
	Annotation         string                          `json:"annotation,omitempty"`
	Version            uint                            `json:"version,omitempty"`
	Steps              map[string]*StoredWorkflowStep  `json:"steps,omitempty"`
	// contains filtered or unexported fields
}

func Get

func Get(ctx context.Context, g *blend4go.GalaxyInstance, id blend4go.GalaxyID) (*StoredWorkflow, error)

Displays information needed to run a workflow.

func List

func List(ctx context.Context, g *blend4go.GalaxyInstance, published, hidden, deleted, missingTools bool) ([]*StoredWorkflow, error)

Get list of workflows published – if True, show also published workflows hidden – if True, show hidden workflows deleted – if True, show deleted workflows missingTools – if True, include a list of missing tools per workflow

func NewStoredWorkflow

func NewStoredWorkflow(ctx context.Context, g *blend4go.GalaxyInstance, j string, importTools, publish, importable bool) (*StoredWorkflow, error)

func (*StoredWorkflow) Delete

func (w *StoredWorkflow) Delete(ctx context.Context) error

Delete a specified workflow

func (*StoredWorkflow) Download

func (w *StoredWorkflow) Download(ctx context.Context) (string, error)

func (*StoredWorkflow) GetBasePath

func (w *StoredWorkflow) GetBasePath() string

func (*StoredWorkflow) GetID

func (w *StoredWorkflow) GetID() blend4go.GalaxyID

func (*StoredWorkflow) Invoke

func (w *StoredWorkflow) Invoke(ctx context.Context) error

Schedule the workflow specified by workflow_id to run.

func (*StoredWorkflow) Repositories

func (w *StoredWorkflow) Repositories(ctx context.Context) ([]*repositories.Repository, error)

func (*StoredWorkflow) SetGalaxyInstance

func (w *StoredWorkflow) SetGalaxyInstance(g *blend4go.GalaxyInstance)

func (*StoredWorkflow) SetID

func (w *StoredWorkflow) SetID(id blend4go.GalaxyID)

func (*StoredWorkflow) Update

func (w *StoredWorkflow) Update(ctx context.Context, j string) error

Update the specified workflow. If json == "", only the name, annotation, and show_in_tool_panel will be updated.

type StoredWorkflowInput

type StoredWorkflowInput struct {
	Uuid  string `json:"uuid,omitempty"`
	Value string `json:"value,omitempty"`
	Label string `json:"label,omitempty"`
}

type StoredWorkflowInputStep

type StoredWorkflowInputStep struct {
	StepOutput string `json:"step_output,omitempty"`
	SourceStep uint   `json:"source_step,omitempty"`
}

type StoredWorkflowStep

type StoredWorkflowStep struct {
	ToolId      string                              `json:"tool_id,omitempty"`
	ToolVersion string                              `json:"tool_version,omitempty"`
	Id          uint                                `json:"id,omitempty"`
	InputSteps  map[string]*StoredWorkflowInputStep `json:"input_steps,omitempty"`
	// ToolInputs	? `json:"tool_inputs,omitempty"` TODO?
	Type       string `json:"type,omitempty"`
	Annotation string `json:"annotation,omitempty"`
}

type WorkflowInvocation

type WorkflowInvocation struct {
	Id         blend4go.GalaxyID `json:"id,omitempty"`
	UpdateTime string            `json:"update_time,omitempty"`
	Uuid       string            `json:"uuid,omitempty"`
	// Outputs ? `json:"outputs,omitempty"`
	// Output_collections ? `json:"output_collections,omitempty"`
	HistoryId  blend4go.GalaxyID `json:"history_id,omitempty"`
	WorkflowId blend4go.GalaxyID `json:"workflow_id,omitempty"`
	State      string            `json:"state,omitempty"`
	ModelClass string            `json:"model_class,omitempty"`
	// Inputs ? `json:"inputs,omitempty"`
	Steps []*WorkflowInvocationStep `json:"steps,omitempty"`
	// contains filtered or unexported fields
}

func (*WorkflowInvocation) GetBasePath

func (w *WorkflowInvocation) GetBasePath() string

func (*WorkflowInvocation) GetID

func (w *WorkflowInvocation) GetID() blend4go.GalaxyID

func (*WorkflowInvocation) SetGalaxyInstance

func (w *WorkflowInvocation) SetGalaxyInstance(g *blend4go.GalaxyInstance)

func (*WorkflowInvocation) SetID

func (w *WorkflowInvocation) SetID(id blend4go.GalaxyID)

type WorkflowInvocationStep

type WorkflowInvocationStep struct {
	Id                   blend4go.GalaxyID                                `json:"id,omitempty"`
	WorkflowStepUuid     string                                           `json:"workflow_step_uuid,omitempty"`
	UpdateTime           string                                           `json:"update_time,omitempty"`
	Jobs                 []*jobs.Job                                      `json:"jobs,omitempty"`
	JobId                string                                           `json:"job_id,omitempty"`
	Outputs              []*histories.HistoryDatasetAssociation           `json:"outputs,omitempty"`
	OrderIndex           uint                                             `json:"order_index,omitempty"`
	OutputCollections    []*histories.HistoryDatasetCollectionAssociation `json:"output_collections,omitempty"`
	WorkflowStepLabel    string                                           `json:"workflow_step_label,omitempty"`
	State                string                                           `json:"state,omitempty"`
	Action               string                                           `json:"action,omitempty"`
	ModelClass           string                                           `json:"model_class,omitempty"`
	WorkflowStepId       blend4go.GalaxyID                                `json:"workflow_step_id,omitempty"`
	WorkflowInvocationId blend4go.GalaxyID                                `json:"workflow_invocation_id,omitempty"`
}