🐛 Set subject_id attribute on Configuration object in anatomical longitudinal workflow

[shnizzedy]

Fixes

Fixes #2156 by @Shinwon Park

Description

1. Updates

   C-PAC/CPAC/longitudinal_pipeline/longitudinal_workflow.py

   Lines 384 to 388 in f8e09b1

   	def anat_longitudinal_wf(
   	subject_id: str, sub_list: list[dict], config: Configuration
   	) -> None:
   	"""
   	Create and run anatomical longitudinal workflow(s).

   to include

   C-PAC/CPAC/longitudinal_pipeline/longitudinal_workflow.py

   Line 400 in f8e09b1

   config["subject_id"] = subject_id

2. Updates

   C-PAC/CPAC/pipeline/engine.py

   Line 1076 in cda28cd

   outputs_logger = getLogger(f'{cfg["subject_id"]}_expectedOutputs')

   to
   

   C-PAC/CPAC/pipeline/engine.py

   Line 1076 in 12daee2

   outputs_logger = getLogger(f'{cfg.get("subject_id", getattr(wf, "name", ""))}_expectedOutputs')

   so subject_id will fall back on the workflow's name if unset, and if that is also unset, fall back on an empty string.

Technical details

This change includes passing the get method through from a Configuration's dict to the Configuration itself:

C-PAC/CPAC/utils/configuration/configuration.py

Lines 257 to 270 in f8e09b1

	def get(self, key: Any, default: Any = None, /) -> Any:
	"""Provide convenience access from `Configuration` to :meth:`dict.get` .
	Examples
	--------
	>>> c = Configuration()
	>>> c.get("subject_id") is None
	True
	>>> c.get("subject_id", "fake_ID")
	'fake_ID'
	>>> isinstance(c.get("pipeline_setup"), dict)
	True
	"""
	return self.dict().get(key, default)

Tests

C-PAC/CPAC/utils/configuration/configuration.py

Lines 262 to 268 in f8e09b1

	>>> c = Configuration()
	>>> c.get("subject_id") is None
	True
	>>> c.get("subject_id", "fake_ID")
	'fake_ID'
	>>> isinstance(c.get("pipeline_setup"), dict)
	True

Checklist

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• My pull request targets the develop branch of the repository.
• My commit messages follow best practices.
• My code follows the established code style of the repository.
• I added tests for the changes I made (if applicable).
• I updated the changelog.
• I added or updated documentation (if applicable).
• I tried running the project locally and verified that there are no visible errors.

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