"""Module containing :func:`convert_and_import_workflow`."""
import os
from .converter import python_to_workflow, yaml_to_workflow
from .interface import BioBlendImporterGalaxyInterface
from .yaml import ordered_load
[docs]def convert_and_import_workflow(has_workflow, **kwds):
"""Conversion and import Format 2 workflows into a target Galaxy instance."""
galaxy_interface = kwds.get("galaxy_interface", None)
if galaxy_interface is None:
galaxy_interface = BioBlendImporterGalaxyInterface(**kwds)
source_type = kwds.get("source_type", None)
workflow_directory = kwds.get("workflow_directory", None)
if source_type == "path":
workflow_path = has_workflow
if workflow_directory is None:
workflow_directory = os.path.dirname(has_workflow)
with open(workflow_path) as f:
has_workflow = ordered_load(f)
if workflow_directory is not None:
workflow_directory = os.path.abspath(workflow_directory)
convert = kwds.get("convert", True)
raw_yaml = kwds.get("raw_yaml", False)
if raw_yaml and convert:
raise Exception("Incompatible options selected.")
if convert:
if isinstance(has_workflow, dict):
workflow = python_to_workflow(has_workflow, galaxy_interface, workflow_directory)
else:
workflow = yaml_to_workflow(has_workflow, galaxy_interface, workflow_directory)
else:
workflow = has_workflow
if not isinstance(workflow, dict) and not raw_yaml:
workflow = ordered_load(workflow)
else:
workflow = {"yaml_content": workflow}
name = kwds.get("name", None)
if name is not None:
workflow["name"] = name
publish = kwds.get("publish", False)
exact_tools = kwds.get("exact_tools", False)
fill_defaults = kwds.get("fill_defaults", True)
import_kwds = {
"fill_defaults": fill_defaults
}
if publish:
import_kwds["publish"] = True
if exact_tools:
import_kwds["exact_tools"] = True
return galaxy_interface.import_workflow(workflow, **import_kwds)
__all__ = (
'convert_and_import_workflow',
)