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Streamflow/RO-Crate parse improvement #143

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Merged
henricasanova merged 2 commits into from
Mar 1, 2026
Merged

Streamflow/RO-Crate parse improvement #143

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ca9f0cb
Re-establishing tests
henricasanova Mar 1, 2026
785f7d3
Ensure Task ID uniqueness in RO-Crate parser
henricasanova Mar 1, 2026
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10 changes: 6 additions & 4 deletions wfcommons/wfinstances/logs/ro_crate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -159,17 +159,17 @@ def _create_tasks(self, create_actions, main_workflow_id):


task = Task(name=create_action['name'],
task_id=create_action['name'],
# task_id=create_action['name'] + "_" + create_action['@id'],
# task_id=create_action['name'],
task_id=create_action['name'] + "_" + create_action['@id'],
task_type=TaskType.COMPUTE,
runtime=self._time_diff(create_action['startTime'], create_action['endTime']),
executed_at=create_action['startTime'],
input_files=self._get_file_objects(input_files),
output_files=self._get_file_objects(output_files),
logger=self.logger)
self.workflow.add_task(task)
self.task_id_name_map[create_action['@id']] = create_action['name']
# self.task_id_name_map[create_action['@id']] = create_action['name'] + "_" + create_action['@id']
# self.task_id_name_map[create_action['@id']] = create_action['name']
self.task_id_name_map[create_action['@id']] = create_action['name'] + "_" + create_action['@id']

# For each file, track which task(s) it is in/output for
for infile in input_files:
Expand Down Expand Up @@ -213,11 +213,13 @@ def _add_dependencies(self, files, instruments):
# source_parameters = parameter_connection["sourceParameter"]
# if not isinstance(source_parameters, list):
# source_parameters = [source_parameters]
# for item in source_parameters:
# source = item["@id"]
# source = source.rsplit("#", 1)[0] # Trim to get instrument
#
# target = parameter_connection["targetParameter"]["@id"]
# target = target.rsplit("#", 1)[0] # Trim to get instrument
# print("source", source, "----> target", target)
#
# for parent in instruments.get(source, []):
# for child in instruments.get(target, []):
Expand Down