def convert_to_workflow(command_line_tool, location=None):
"""
Converts "command_line_tool" to Workflow trying to keep all
important elements. If "command_line_tool" is already Workflow,
doesn't apply any changes. If "location" is not None, dumps
results to json file.
"""
if command_line_tool["class"] == "Workflow":
workflow_tool = command_line_tool
else:
workflow_tool = {
"class": "Workflow",
"cwlVersion": command_line_tool["cwlVersion"],
"inputs": [],
"outputs": []
}
for key in ["requirements"]:
if key in command_line_tool:
workflow_tool[key] = command_line_tool[key]
for input_id, input_data in get_items(command_line_tool["inputs"]):
workflow_input = {
"id": input_id,
"type": remove_field_from_dict(
input_data["type"], "inputBinding"
) # "type" in WorkflowInputParameter cannot have "inputBinding"
}
for key in ["secondaryFiles",
"default"]: # TODO: Do I need to copy format?
if key in input_data:
workflow_input[key] = input_data[key]
workflow_tool["inputs"].append(workflow_input)
for output_id, output_data in get_items(command_line_tool["outputs"]):
workflow_output = {
"id":
output_id,
"type":
output_data["type"],
"outputSource":
get_rootname(command_line_tool["id"]) + "/" + output_id
}
# TODO: not sure if I need format here
# for key in ["format"]:
# if key in output_data:
# workflow_output[key] = output_data[key]
workflow_tool["outputs"].append(workflow_output)
workflow_tool["steps"] = [{
"id":
get_rootname(command_line_tool["id"]),
"run":
command_line_tool,
"in": [{
"id": input_id,
"source": input_id
} for input_id, _ in get_items(workflow_tool["inputs"])],
"out": [
output_id
for output_id, _ in get_items(workflow_tool["outputs"])
]
}]
if location is not None:
dump_json(workflow_tool, location)
return workflow_tool
def test_remove_field_from_dict(data, key, control_data):
clean_data = remove_field_from_dict(data, key)
assert all(control_data[key] == value for key, value in
clean_data.items()), "Failed to remove field from dictionary"