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fix step_key evaluation in get_workflow_outputs #246

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merged 1 commit into from
Jun 24, 2024
+8 −3
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fix step_key evaluation in get_workflow_outputs #246

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3 changes: 2 additions & 1 deletion src/sophios/compiler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -833,7 +833,8 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
vars_workflow_output_internal = list(set(vars_workflow_output_internal)) # Get uniques
# (Why are we getting uniques?)
workflow_outputs = utils_cwl.get_workflow_outputs(args, namespaces, is_root, yaml_stem,
steps, outputs_workflow, vars_workflow_output_internal, graph, tools_lst, step_node_name)
steps, outputs_workflow, vars_workflow_output_internal,
graph, tools_lst, step_node_name, tools)
# Add the provided workflow outputs to the workflow outputs from each step
outputs_combined = {**yaml_tree.get('outputs', {}), **workflow_outputs}
yaml_tree.update({'outputs': outputs_combined})
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8 changes: 6 additions & 2 deletions src/sophios/utils_cwl.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

from . import utils
from .wic_types import (GraphReps, InternalOutputs, Namespaces, Tool, Tools,
WorkflowOutputs, Yaml)
WorkflowOutputs, Yaml, StepId)


def maybe_add_requirements(yaml_tree: Yaml, steps_keys: List[str],
Expand Down Expand Up @@ -110,7 +110,8 @@ def get_workflow_outputs(args: argparse.Namespace,
vars_workflow_output_internal: InternalOutputs,
graph: GraphReps,
tools_lst: List[Tool],
step_node_name: str) -> Dict[str, Dict[str, str]]:
step_node_name: str,
tools: Tools) -> Dict[str, Dict[str, str]]:
"""Chooses a subset of the CWL outputs: to actually output

Args:
Expand All @@ -125,6 +126,7 @@ def get_workflow_outputs(args: argparse.Namespace,
graph (GraphReps): A tuple of a GraphViz DiGraph and a networkx DiGraph
tools_lst (List[Tool]): A list of the CWL CommandLineTools or compiled subworkflows for the current workflow.
step_node_name (str): The namespaced name of the current step
tools (Tools): The CWL CommandLineTool definitions found using get_tools_cwl()

Returns:
Dict[str, Dict[str, str]]: The actual outputs to be specified in the generated CWL file
Expand All @@ -135,7 +137,9 @@ def get_workflow_outputs(args: argparse.Namespace,
for i, step_key in enumerate(steps_keys):
tool_i = tools_lst[i].cwl
step_name_i = utils.step_name_str(yaml_stem, i, step_key)
step_id = StepId(Path(step_key).stem, 'global')
step_name_or_key = step_name_i if step_key.endswith('.wic') \
or step_id in tools \
or Path(step_key).stem == Path(tools_lst[i].run_path).stem else step_key
# step_name_or_key = step_name_i if stepid in tools else step_key
out_keys = steps[i]['out']
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