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`.
59 lines
2 KiB
Python
59 lines
2 KiB
Python
import os
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import re
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def fix_dangling_in_file(path):
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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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# keys that take lists
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list_keys = [
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"slots",
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"exact_mappings", "close_mappings", "broad_mappings", "related_mappings", "narrow_mappings",
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"examples", "comments", "see_also", "keywords", "structured_aliases",
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"subsets", "mixins", "apply_to", "union_of", "values", "equals_expression", "equals_string_in",
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"aliases", "local_names", "union_of", "defines"
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]
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last_key_at_4 = None
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for i, line in enumerate(lines):
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stripped = line.strip()
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if not stripped or stripped.startswith('#'):
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new_lines.append(line)
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continue
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indent = len(line) - len(line.lstrip())
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# Check if line is a key at 4 spaces
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# Regex: start with 4 spaces, then key chars, then colon, then optional space/value
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if indent == 4 and ':' in stripped and not stripped.startswith('-'):
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key = stripped.split(':')[0].strip()
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last_key_at_4 = key
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new_lines.append(line)
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continue
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# Check if line is a list item at 4 spaces
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if indent == 4 and stripped.startswith('-'):
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if last_key_at_4 not in list_keys:
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print(f"Removing dangling list item in {path} at line {i+1} (after {last_key_at_4}): {stripped}")
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continue # Skip/Delete
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# Reset last_key_at_4 if indentation drops below 4
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if indent < 4:
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last_key_at_4 = None
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new_lines.append(line)
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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_dangling_in_file(os.path.join(root, file))
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process_directory("schemas/20251121/linkml/modules/classes")
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