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`.
48 lines
1.4 KiB
Python
48 lines
1.4 KiB
Python
import os
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def fix_file(path):
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filename = os.path.basename(path)
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classname = filename.replace('.yaml', '')
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with open(path, 'r') as f:
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lines = f.readlines()
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new_lines = []
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in_imports = False
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modified = False
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for line in lines:
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stripped = line.strip()
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if stripped == "imports:":
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in_imports = True
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new_lines.append(line)
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continue
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if in_imports:
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if not stripped.startswith("-"):
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if stripped and not stripped.startswith("#"):
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in_imports = False
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new_lines.append(line)
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else:
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import_path = stripped.lstrip("- ").strip()
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# Check for self-import: - ./ClassName
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if import_path == f"./{classname}":
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print(f"Removing self-import in {path}: {stripped}")
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modified = True
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continue
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else:
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new_lines.append(line)
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else:
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new_lines.append(line)
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if modified:
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with open(path, 'w') as f:
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f.writelines(new_lines)
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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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fix_file(os.path.join(root, file))
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process_directory("schemas/20251121/linkml/modules/classes")
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