🐛 Fix parsing FROM: /filepath

[shnizzedy]

Fixes

Fixes FileNotFoundError: [Errno 2] No such file or directory: '/code/CPAC/resources/configs/pipeline_config_/configs/pipeline_config_cpac_1.8.5_fromPhoebeNoDeriviativesNative.yml.yml' by @Shinwon Park

Technical details

Consolidates

C-PAC/CPAC/utils/utils.py

Lines 1518 to 1542 in ecfc583

	def load_preconfig(pipeline_label):
	import os
	import pkg_resources as p
	if pipeline_label not in ALL_PIPELINE_CONFIGS:
	raise BadParameter(
	"The pre-configured pipeline name '{0}' you provided is not one "
	"of the available pipelines.\n\nAvailable pipelines:\n"
	"{1}\n".format(pipeline_label, str(AVAILABLE_PIPELINE_CONFIGS)),
	param='preconfig')
	pipeline_file = \
	p.resource_filename(
	"CPAC",
	os.path.join(
	"resources",
	"configs",
	"pipeline_config_{0}.yml".format(pipeline_label)
	)
	)
	print(f"Loading the '{pipeline_label}' pre-configured pipeline.",
	file=sys.stderr)
	return pipeline_file

and

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

Lines 606 to 625 in ecfc583

	def preconfig_yaml(preconfig_name='default', load=False):
	"""Get the path to a preconfigured pipeline's YAML file
	Parameters
	----------
	preconfig_name : str
	load : boolean
	return dict if True, str if False
	Returns
	-------
	str or dict
	path to YAML file or dict loaded from YAML
	"""
	if load:
	with open(preconfig_yaml(preconfig_name), 'r', encoding='utf-8') as _f:
	return yaml.safe_load(_f)
	return p.resource_filename("CPAC", os.path.join(
	"resources", "configs", f"pipeline_config_{preconfig_name}.yml"))

into

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

Lines 620 to 647 in 907fab5

	def preconfig_yaml(preconfig_name='default', load=False):
	"""Get the path to a preconfigured pipeline's YAML file.
	Raises BadParameter if an invalid preconfig name is given.
	Parameters
	----------
	preconfig_name : str
	load : boolean
	return dict if True, str if False
	Returns
	-------
	str or dict
	path to YAML file or dict loaded from YAML
	"""
	from CPAC.pipeline import ALL_PIPELINE_CONFIGS, AVAILABLE_PIPELINE_CONFIGS
	if preconfig_name not in ALL_PIPELINE_CONFIGS:
	raise BadParameter(
	"The pre-configured pipeline name '{0}' you provided is not one "
	"of the available pipelines.\n\nAvailable pipelines:\n"
	f"{1}\n".format(preconfig_name, str(AVAILABLE_PIPELINE_CONFIGS)),
	param='preconfig')
	if load:
	with open(preconfig_yaml(preconfig_name), 'r', encoding='utf-8') as _f:
	return yaml.safe_load(_f)
	return p.resource_filename("CPAC", os.path.join(
	"resources", "configs", f"pipeline_config_{preconfig_name}.yml"))

so preconfiguration loading is handled consistently everywhere and updates the relevant function calls.

Tests

C-PAC/CPAC/utils/tests/configs/__init__.py

Lines 15 to 21 in 907fab5

	# A loaded YAML file to test https://tinyurl.com/cmicnlslack420349
	SLACK_420349 = {
	"filepath": yaml.dump({
	"FROM": str(_TEST_CONFIGS_PATH / "neurostars_23786.yml"),
	"pipeline_setup": {"pipeline_name": "slack_420349_filepath"}}),
	"preconfig": yaml.dump({"FROM": "preproc",
	"pipeline_setup": {"pipeline_name": "slack_420349_preconfig"}})}

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

Lines 88 to 100 in 907fab5

	>>> from CPAC.utils.tests.configs import SLACK_420349
	# test "FROM: /path/to/file"
	>>> slack_420349_filepath = Configuration(
	... yaml.safe_load(SLACK_420349['filepath']))
	>>> slack_420349_filepath['pipeline_setup', 'pipeline_name']
	'slack_420349_filepath'
	# test "FROM: preconfig"
	>>> slack_420349_preconfig = Configuration(
	... yaml.safe_load(SLACK_420349['preconfig']))
	>>> slack_420349_preconfig['pipeline_setup', 'pipeline_name']
	'slack_420349_preconfig'

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
• 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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[shnizzedy]

The ACCESS deployments are "failure"s because I rejected them ― these changes shouldn't affect anything that those would cover