mirror of
https://github.com/galaxyproject/galaxy.git
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John Chilton
a0177fe2f4
Needed to test workflow tool upgrades when loading workflows, but I think it is good to have a way to preserve the original tool state as well for the sake of absolute reproducibility/tracibility.
46 lines
1.5 KiB
Python
46 lines
1.5 KiB
Python
"""Module containing :func:`convert_and_import_workflow`."""
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import os
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import yaml
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from .converter import python_to_workflow, yaml_to_workflow
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from .interface import BioBlendImporterGalaxyInterface
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def convert_and_import_workflow(has_workflow, **kwds):
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"""Function is main entry for conversion and import of Format 2 workflows."""
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galaxy_interface = kwds.get("galaxy_interface", None)
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if galaxy_interface is None:
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galaxy_interface = BioBlendImporterGalaxyInterface(**kwds)
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source_type = kwds.get("source_type", None)
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workflow_directory = kwds.get("workflow_directory", None)
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if source_type == "path":
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workflow_path = has_workflow
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if workflow_directory is None:
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workflow_directory = os.path.dirname(has_workflow)
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with open(workflow_path, "r") as f:
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has_workflow = yaml.load(f)
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if workflow_directory is not None:
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workflow_directory = os.path.abspath(workflow_directory)
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if isinstance(has_workflow, dict):
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workflow = python_to_workflow(has_workflow, galaxy_interface, workflow_directory)
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else:
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workflow = yaml_to_workflow(has_workflow, galaxy_interface, workflow_directory)
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publish = kwds.get("publish", False)
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exact_tools = kwds.get("exact_tools", False)
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import_kwds = {}
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if publish:
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import_kwds["publish"] = True
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if exact_tools:
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import_kwds["exact_tools"] = True
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return galaxy_interface.import_workflow(workflow, **import_kwds)
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__all__ = (
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'convert_and_import_workflow',
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)
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