fc405445c6
- Removed obsolete slots: `has_or_had_custodian_observation`, `provider`, and `specificity_annotation`. - Updated `has_or_had_score` slot to use `SpecificityScore` class and modified its description and examples. - Added new slots: `end_seconds`, `end_time`, `has_archive_path`, `has_or_had_custodian_name`, `protocol_name`, and `protocol_version`. - Introduced a script `check_annotation_types.py` to validate the presence and structure of `custodian_types` in YAML files. - Added a script `update_specificity.py` to automate updates related to `SpecificityAnnotation` to `SpecificityScore`.
33 lines
1 KiB
Python
33 lines
1 KiB
Python
import yaml
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import os
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def check_dict(d, path, context="root"):
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if not isinstance(d, dict):
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return
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for k, v in d.items():
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if k == 'custodian_types':
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if context != 'annotations':
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print(f"Misplaced custodian_types in {path} at context '{context}'")
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if isinstance(v, dict):
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check_dict(v, path, k)
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elif isinstance(v, list):
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for item in v:
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check_dict(item, path, k)
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def process_directory(directory):
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for root, dirs, files in os.walk(directory):
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for file in files:
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if file.endswith(".yaml"):
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path = os.path.join(root, file)
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try:
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with open(path, 'r') as f:
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data = yaml.safe_load(f)
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check_dict(data, path)
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except Exception as e:
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# Ignore parse errors
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pass
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process_directory("schemas/20251121/linkml/modules/classes")
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process_directory("schemas/20251121/linkml/modules/slots")
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