def test_describe_outputs():
wf_path = os.path.join(TEST_DATA_DIR, "wf1.gxwf.yml")
outputs = describe_outputs(wf_path)
assert len(outputs) == 1
output = outputs[0]
assert output.order_index == 1
assert output.output_name == "out_file1"
assert output.label == "wf_output_1"
def get_outputs(runnable):
"""Return a list of :class:`RunnableOutput` objects for this runnable."""
if not runnable.is_single_artifact:
raise NotImplementedError("Cannot generate outputs for a directory.")
if runnable.type in [RunnableType.galaxy_tool, RunnableType.cwl_tool]:
tool_source = get_tool_source(runnable.path)
# TODO: do something with collections at some point
output_datasets, _ = tool_source.parse_outputs(None)
return [ToolOutput(o) for o in output_datasets.values()]
elif runnable.type == RunnableType.galaxy_workflow:
workflow_outputs = describe_outputs(runnable.path)
return [GalaxyWorkflowOutput(o) for o in workflow_outputs]
else:
raise NotImplementedError("Getting outputs for this artifact type is not yet supported.")
def get_outputs(runnable):
"""Return a list of :class:`RunnableOutput` objects for this runnable."""
if not runnable.is_single_artifact:
raise NotImplementedError("Cannot generate outputs for a directory.")
if runnable.type in [RunnableType.galaxy_tool, RunnableType.cwl_tool]:
tool_source = get_tool_source(runnable.path)
# TODO: do something with collections at some point
output_datasets, _ = tool_source.parse_outputs(None)
return [ToolOutput(o) for o in output_datasets.values()]
elif runnable.type == RunnableType.galaxy_workflow:
workflow_outputs = describe_outputs(runnable.path)
return [GalaxyWorkflowOutput(o) for o in workflow_outputs]
else:
raise NotImplementedError("Getting outputs for this artifact type is not yet supported.")
def get_outputs(runnable, gi=None):
"""Return a list of :class:`RunnableOutput` objects for this runnable.
Supply bioblend user Galaxy instance object (as gi) if additional context
needed to resolve workflow details.
"""
if not runnable.is_single_artifact:
raise NotImplementedError("Cannot generate outputs for a directory.")
if runnable.type in [RunnableType.galaxy_tool, RunnableType.cwl_tool]:
tool_source = get_tool_source(runnable.path)
# TODO: do something with collections at some point
output_datasets, _ = tool_source.parse_outputs(None)
outputs = [ToolOutput(o) for o in output_datasets.values()]
return outputs
elif runnable.type == RunnableType.galaxy_workflow:
workflow_outputs = describe_outputs(runnable, gi=gi)
return [GalaxyWorkflowOutput(o) for o in workflow_outputs]
elif runnable.type == RunnableType.cwl_workflow:
workflow = workflow_proxy(runnable.path, strict_cwl_validation=False)
return [CwlWorkflowOutput(label) for label in workflow.output_labels]
else:
raise NotImplementedError(
"Getting outputs for this artifact type is not yet supported.")
