Export a Workflow to a Portable Zip File

This function exports a workflow to a zip file that can be imported into another repository. It preserves workflow structure, step dependencies, file relationships, and includes all necessary files for reconstruction in a different environment.

Usage

exportWorkflow(workflow, workflowName, targetFolder = ".")

Arguments

workflow

Workflow environment object created by createWorkflow containing the steps and their relationships to export.

workflowName

Character. Name for the exported workflow (without extension). This will be used as the zip filename and internal folder name.

targetFolder

Character. Directory path where the zip file will be created. Defaults to current directory (".").

Value

Character. Path to the created zip file.

Details

The export process includes the following steps:

1. Creates a workflow template from the provided workflow

2. Creates a temporary export directory structure

3. Generates workflow.json with complete step definitions

4. Exports internal links between steps to internalLinks.json

5. Downloads and includes external link files

6. Clones each step's input and output files

7. Creates mapping templates for links and tools

8. Packages everything into a single zip file

Export Structure

The exported zip file contains:

• workflow.json - Complete workflow metadata and step definitions

• internalLinks.json - Dependencies between workflow steps

• links/ - Directory containing external file dependencies

• Step folders (named by handle) containing:

  • inputFiles/ - Input files for the step

  • outputFiles/ - Output files from the step execution

Generated Mapping Templates

The function also creates template mapping files alongside the zip:

LinkMapping.json - Template for mapping external files:

[
  {
    "key": "file-identifier",
    "ident": "",  # Fill in target repository resource ID
    "name": "original-filename",
    "hash": "file-hash-for-validation"
  }
]

ToolMapping.json - Template for tool configuration mapping:

[
  {
    "key": "server:::tool:::instance:::gridTool",
    "runserverLabel": "",  # Fill in target server
    "toolLabel": "",       # Fill in target tool
    "toolInstance": "",    # Fill in target instance
    "gridTool": true/false
  }
]

See also

importWorkflow for importing exported workflows

Examples

if (FALSE) { # \dontrun{
# Create and export a workflow
wf <- createWorkflow()
# ... add steps to workflow ...

# Export to current directory
exportWorkflow(wf, "myWorkflow")
# Creates: myWorkflow.zip, myWorkflowLinkMapping.json, myWorkflowToolMapping.json

# Export to specific directory
exportWorkflow(wf, "analysis_v2", targetFolder = "/exports/workflows")

# The generated mapping files can be edited before import to:
# - Point links to existing resources in target repository
# - Map tools to different compute servers
# - Adapt to different environment configurations
} # }