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`.
50 lines
2.1 KiB
Python
50 lines
2.1 KiB
Python
import yaml
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import os
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def check_file(path):
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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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except Exception as e:
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print(f"Error parsing {path}: {e}")
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return
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if 'classes' in data:
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for class_name, class_def in data['classes'].items():
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if 'custodian_types' in class_def:
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print(f"Misplaced custodian_types found in {path} Class {class_name} (root level)")
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if 'slot_usage' in class_def and class_def['slot_usage']:
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for slot_name, slot_def in class_def['slot_usage'].items():
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if slot_def and 'custodian_types' in slot_def:
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print(f"Misplaced custodian_types found in {path} Class {class_name} SlotUsage {slot_name}")
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if 'annotations' in class_def:
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ann = class_def['annotations']
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if ann and 'custodian_types' in ann:
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val = ann['custodian_types']
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if isinstance(val, list):
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print(f"List value found in {path} Class {class_name}: {val}")
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elif not isinstance(val, str):
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print(f"Non-string value found in {path} Class {class_name}: {val} (type: {type(val)})")
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if 'slots' in data:
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for slot_name, slot_def in data['slots'].items():
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if 'custodian_types' in slot_def:
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print(f"Misplaced custodian_types found in {path} Slot {slot_name} (root level)")
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if 'annotations' in slot_def:
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ann = slot_def['annotations']
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if ann and 'custodian_types' in ann:
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val = ann['custodian_types']
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if isinstance(val, list):
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print(f"List value found in {path} Slot {slot_name}: {val}")
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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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check_file(os.path.join(root, file))
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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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