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Drop old hack, we're extracting HDAs for DCEs just fine these days
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@@ -1925,7 +1925,6 @@ class ToolModule(WorkflowModule):
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all_inputs_by_name = {}
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for input_dict in all_inputs:
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all_inputs_by_name[input_dict["name"]] = input_dict
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# do some magic here with incoming collection info
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collection_info = self.compute_collection_info(progress, step, all_inputs)
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param_combinations = []
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@@ -1950,19 +1949,7 @@ class ToolModule(WorkflowModule):
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replacement: Union[model.Dataset, NoReplacement] = NO_REPLACEMENT
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dataset_instance: Optional[model.Dataset] = None
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if iteration_elements and prefixed_name in iteration_elements: # noqa: B023
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dataset_instance = getattr(
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iteration_elements[prefixed_name], "dataset_instance", None # noqa: B023
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)
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if isinstance(input, DataToolParameter) and dataset_instance:
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# Pull out dataset instance (=HDA) from element and set a temporary element_identifier attribute
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# See https://github.com/galaxyproject/galaxy/pull/1693 for context.
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replacement = dataset_instance
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temp = iteration_elements[prefixed_name] # noqa: B023
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if hasattr(temp, "element_identifier") and temp.element_identifier:
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replacement.element_identifier = temp.element_identifier # type: ignore[union-attr]
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else:
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# If collection - just use element model object.
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replacement = iteration_elements[prefixed_name] # noqa: B023
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replacement = iteration_elements[prefixed_name] # noqa: B023
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else:
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replacement = progress.replacement_for_input(step, input_dict)
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@@ -3105,10 +3105,9 @@ test_data:
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assert len(elements) == 2
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assert elements[0]["element_identifier"] == "1"
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assert elements[0]["element_type"] == "hda"
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# FIXME: make this work!
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# hda_id = elements[0]["object"]["id"]
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# hda_content = self.dataset_populator.get_history_dataset_content(history_id, content_id=hda_id)
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# assert hda_content == "1"
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hda_id = elements[0]["object"]["id"]
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hda_content = self.dataset_populator.get_history_dataset_content(history_id, content_id=hda_id)
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assert hda_content.strip() == "1"
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@skip_without_tool("identifier_multiple")
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def test_invocation_map_over_inner_collection(self, history_id):
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