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Fix provenance handling for secondary files #1068

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Fix provenance handling for secondary files #1068

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Fixed

- Fix provenance handling for secondary files ([#1068](https://github.com/alpha-unito/streamflow/pull/1068))
- Fix bind mount inspection in `SingularityConnector` ([#1058](https://github.com/alpha-unito/streamflow/pull/1058))
- Fix `--wait` flag in `Helm4Connector` for Cobra parser ([#1050](https://github.com/alpha-unito/streamflow/pull/1050))
- Fix shell reuse collision across execution locations ([#1045](https://github.com/alpha-unito/streamflow/pull/1045))
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23 changes: 13 additions & 10 deletions streamflow/provenance/run_crate.py
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Expand Up @@ -1483,16 +1483,19 @@ async def get_property_value(
)
value = []
for property_value in (k for k in property_values if k is not None):
if property_value["@type"] in ["Dataset", "File"]:
# Check for duplicate checksums
if property_value["@id"] not in self.graph:
self.graph["./"]["hasPart"].append(
{"@id": property_value["@id"]}
)
self.graph[property_value["@id"]] = property_value
value.append({"@id": property_value["@id"]})
else:
value.append(property_value["value"])
match property_value["@type"]:
case "Collection":
value.append({"@id": property_value["@id"]})
case "Dataset" | "File":
# Check for duplicate checksums
if property_value["@id"] not in self.graph:
self.graph["./"]["hasPart"].append(
{"@id": property_value["@id"]}
)
self.graph[property_value["@id"]] = property_value
value.append({"@id": property_value["@id"]})
case _:
value.append(property_value["value"])
value = streamflow.core.utils.flatten_list(value)
return {
"@id": "#" + str(uuid.uuid4()),
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