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Fixed InplaceUpdateRequirement in the distributed executions #467

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Fixed InplaceUpdateRequirement in the distributed executions #467

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3 changes: 3 additions & 0 deletions streamflow/cwl/processor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -369,6 +369,7 @@ def __init__(
file_format: str | None = None,
full_js: bool = False,
glob: str | None = None,
inplace_update: bool = False,
load_contents: bool = False,
load_listing: LoadListing = LoadListing.no_listing,
optional: bool = False,
Expand All @@ -382,6 +383,7 @@ def __init__(
self.expression_lib: MutableSequence[str] | None = expression_lib
self.file_format: str | None = file_format
self.full_js: bool = full_js
self.inplace_update: bool = inplace_update
self.glob: str | None = glob
self.load_contents: bool = load_contents
self.load_listing: LoadListing = load_listing
Expand Down Expand Up @@ -446,6 +448,7 @@ async def _build_token(
base_path=(
self.target.workdir if self.target else job.output_directory
),
inplace_update=self.inplace_update,
)
# Process file format
if self.file_format:
Expand Down
9 changes: 9 additions & 0 deletions streamflow/cwl/translator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -208,6 +208,9 @@ def _create_command_output_processor_base(
glob=cwl_element.get("outputBinding", {}).get(
"glob", cwl_element.get("path")
),
inplace_update=context["requirements"]
.get("InplaceUpdateRequirement", {})
.get("inplaceUpdate", False),
load_contents=cwl_element.get(
"loadContents",
cwl_element.get("outputBinding", {}).get("loadContents", False),
Expand All @@ -231,6 +234,9 @@ def _create_command_output_processor_base(
glob=cwl_element.get("outputBinding", {}).get(
"glob", cwl_element.get("path")
),
inplace_update=context["requirements"]
.get("InplaceUpdateRequirement", {})
.get("inplaceUpdate", False),
load_contents=cwl_element.get(
"loadContents",
cwl_element.get("outputBinding", {}).get("loadContents", False),
Expand Down Expand Up @@ -296,6 +302,9 @@ def _create_command_output_processor(
expression_lib=expression_lib,
full_js=full_js,
optional=optional,
inplace_update=context["requirements"]
.get("InplaceUpdateRequirement", {})
.get("inplaceUpdate", False),
)
# Record type: -> ObjectCommandOutputProcessor
elif port_type["type"] == "record":
Expand Down
7 changes: 7 additions & 0 deletions streamflow/cwl/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -177,9 +177,14 @@ async def _register_path(
path: str,
relpath: str,
data_type: DataType = DataType.PRIMARY,
inplace_update: bool = False,
) -> DataLocation | None:
if real_path := await remotepath.follow_symlink(context, connector, location, path):
if real_path != path:
if inplace_update:
for data_loc in context.data_manager.get_data_locations(path=real_path):
if data_loc.deployment != connector.deployment_name:
data_loc.data_type = DataType.INVALID
if data_locations := context.data_manager.get_data_locations(
path=real_path, deployment=connector.deployment_name
):
Expand Down Expand Up @@ -810,6 +815,7 @@ async def register_data(
locations: MutableSequence[ExecutionLocation],
base_path: str | None,
token_value: MutableSequence[MutableMapping[str, Any]] | MutableMapping[str, Any],
inplace_update: bool = False,
):
# If `token_value` is a list, process every item independently
if isinstance(token_value, MutableSequence):
Expand Down Expand Up @@ -860,6 +866,7 @@ async def register_data(
location=location,
path=path,
relpath=relpath,
inplace_update=inplace_update,
)
)
for location in locations
Expand Down
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