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CWL: Fix step input valueFrom with loadContents: true #5570

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CWL: Fix step input valueFrom with loadContents: true #5570

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647a76e
Fix failing read of toildir in ValueFrom.eval_prep when loadContents …
CGuichard Aug 19, 2026
2fd0a8c
Restrict ValueFrom.eval_prep to load only one step input instead of a…
CGuichard Aug 19, 2026
68c72ac
Support step input loadContents for File array (#5568)
CGuichard Aug 21, 2026
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51 changes: 27 additions & 24 deletions src/toil/cwl/cwltoil.py
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Original file line number Diff line number Diff line change
Expand Up @@ -638,35 +638,37 @@ def __repr__(self) -> str:
return f"ValueFrom({self.expr}, {self.source}, {self.req}, {self.container_engine})"

def eval_prep(
self, step_inputs: CWLObjectType, file_store: AbstractFileStore
self, step_input: CWLObjectType, file_store: AbstractFileStore
) -> None:
"""
Resolve the contents of any file in a set of inputs.
Prepare the step_input object before evaluation of valueFrom expression.

The inputs must be associated with the ValueFrom object's self.source.
Responsible for checking loadContents, when enabled load the contents
if the input is of type File/File[].

Called when loadContents is specified.

:param step_inputs: Workflow step inputs.
:param step_input: step input.
:param file_store: A toil file store, needed to resolve toilfile:// paths.
"""
for v in step_inputs.values():
val = cast(CWLObjectType, v)
values = step_input if isinstance(step_input, MutableSequence) else [step_input]
for val in values:
source_input = getattr(self.source, "input", {})
if isinstance(val, dict) and isinstance(source_input, dict):
if (
val.get("contents") is None
and source_input.get("loadContents") is True
):
# This is safe to use even if we're bypassing the file
# store for the workflow. In that case, no toilfile:// or
# other special URIs will exist in the workflow to be read
# from, and ToilFsAccess still supports file:// URIs.
fs_access = functools.partial(ToilFsAccess, file_store=file_store)
with fs_access("").open(cast(str, val["location"]), "rb") as f:
val["contents"] = cwltool.builder.content_limit_respected_read(
f
)
if (
isinstance(val, dict)
and isinstance(source_input, dict)
and val.get("class") == "File"
and val.get("contents") is None
and val.get("location") is not None
and source_input.get("loadContents") is True
):
# This is safe to use even if we're bypassing the file
# store for the workflow. In that case, no toilfile:// or
# other special URIs will exist in the workflow to be read
# from, and ToilFsAccess still supports file:// URIs.
fs_access = functools.partial(ToilFsAccess, file_store=file_store)
with fs_access("").open(cast(str, val["location"]), "rb") as f:
val["contents"] = cwltool.builder.content_limit_respected_read(
f
)

def resolve(self) -> Any:
"""
Expand Down Expand Up @@ -768,8 +770,9 @@ def resolve_dict_w_promises(
result: CWLObjectType = {}
for k, v in dict_w_promises.items():
if isinstance(v, ValueFrom):
if file_store:
v.eval_prep(first_pass_results, file_store)
if file_store and first_pass_results[k]:
step_input = cast(CWLObjectType, first_pass_results[k])
v.eval_prep(step_input, file_store)
result[k] = v.do_eval(inputs=first_pass_results)
else:
result[k] = first_pass_results[k]
Expand Down